Starting phenix.real_space_refine on Mon Sep 14 12:00:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zk9_11241/09_2026/6zk9_11241_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zk9_11241/09_2026/6zk9_11241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zk9_11241/09_2026/6zk9_11241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zk9_11241/09_2026/6zk9_11241.map" model { file = "/net/cci-nas-00/data/ceres_data/6zk9_11241/09_2026/6zk9_11241_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zk9_11241/09_2026/6zk9_11241_neut.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 13 5.49 5 S 188 5.16 5 C 17801 2.51 5 N 4889 2.21 5 O 6666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29587 Number of models: 1 Model: "" Number of chains: 45 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3047 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 245 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 4, 'TRANS': 26} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "2" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "3" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 285 Classifications: {'water': 285} Link IDs: {None: 284} Chain: "4" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 200 Classifications: {'water': 200} Link IDs: {None: 199} Chain: "5" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "6" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "9" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "a" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "b" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "c" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "d" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "e" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "g" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "h" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 76.543 53.579 111.864 1.00 35.70 S ATOM 2695 SG CYS 1 362 78.851 53.632 106.580 1.00 50.14 S ATOM 2676 SG CYS 1 359 83.775 53.674 112.497 1.00 52.93 S ATOM 3039 SG CYS 1 405 80.358 47.743 110.807 1.00 47.41 S ATOM 4116 SG CYS 2 103 74.552 48.610 130.636 1.00 57.20 S ATOM 4150 SG CYS 2 108 72.542 46.250 132.831 1.00 60.11 S ATOM 4430 SG CYS 2 144 76.031 44.903 127.052 1.00 71.98 S ATOM 4453 SG CYS 2 148 74.232 42.140 128.574 1.00 58.51 S ATOM 5793 SG CYS 3 114 79.009 71.894 97.053 1.00 42.51 S ATOM 5732 SG CYS 3 105 73.856 75.366 99.064 1.00 46.29 S ATOM 5753 SG CYS 3 108 80.029 76.829 100.879 1.00 31.92 S ATOM 6125 SG CYS 3 156 86.138 64.291 101.677 1.00 37.88 S ATOM 6102 SG CYS 3 153 84.204 67.270 107.389 1.00 38.57 S ATOM 6149 SG CYS 3 159 90.259 67.901 105.566 1.00 72.59 S ATOM 6479 SG CYS 3 203 86.185 70.521 101.877 1.00 35.52 S ATOM 5238 SG CYS 3 41 85.169 57.774 99.890 1.00 33.03 S ATOM 5324 SG CYS 3 52 81.457 58.986 98.931 1.00 42.22 S ATOM 5349 SG CYS 3 55 81.828 53.979 95.600 1.00 37.68 S ATOM 5450 SG CYS 3 69 85.456 54.021 96.936 1.00 41.26 S ATOM 15270 SG CYS 6 55 58.249 101.716 76.827 1.00 60.47 S ATOM 15768 SG CYS 6 119 64.232 97.547 74.960 1.00 60.54 S ATOM 15998 SG CYS 6 149 61.254 95.551 79.932 1.00 43.23 S ATOM 15264 SG CYS 6 54 57.455 95.447 74.102 1.00 92.29 S ATOM 17190 SG CYS 9 116 65.210 96.301 86.227 1.00 54.58 S ATOM 17237 SG CYS 9 122 65.787 91.834 91.009 1.00 37.48 S ATOM 16964 SG CYS 9 87 69.661 91.531 85.677 1.00 32.10 S ATOM 17266 SG CYS 9 126 67.930 88.448 98.200 1.00 25.33 S ATOM 16937 SG CYS 9 83 71.547 90.077 93.043 1.00 39.44 S ATOM 16895 SG CYS 9 77 73.752 91.612 98.861 1.00 32.31 S ATOM 16914 SG CYS 9 80 72.883 85.127 96.843 1.00 36.56 S ATOM 18513 SG CYS b 59 69.772 84.146 113.454 1.00 48.78 S ATOM 18691 SG CYS b 84 72.713 84.076 111.023 1.00 39.82 S ATOM 18713 SG CYS b 87 71.049 87.104 111.945 1.00 45.15 S Time building chain proxies: 5.92, per 1000 atoms: 0.20 Number of scatterers: 29587 At special positions: 0 Unit cell: (149, 159, 161.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 188 16.00 P 13 15.00 O 6666 8.00 N 4889 7.00 C 17801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 32 sheets defined 45.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain '1' and resid 16 through 20 Processing helix chain '1' and resid 32 through 38 Processing helix chain '1' and resid 44 through 50 Processing helix chain '1' and resid 51 through 64 removed outlier: 4.128A pdb=" N TRP 1 55 " --> pdb=" O LYS 1 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY 1 64 " --> pdb=" O VAL 1 60 " (cutoff:3.500A) Processing helix chain '1' and resid 74 through 80 Processing helix chain '1' and resid 105 through 114 removed outlier: 3.855A pdb=" N GLU 1 109 " --> pdb=" O CYS 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 114 through 129 Processing helix chain '1' and resid 142 through 159 Processing helix chain '1' and resid 165 through 169 Processing helix chain '1' and resid 183 through 187 Processing helix chain '1' and resid 188 through 197 Processing helix chain '1' and resid 214 through 218 Processing helix chain '1' and resid 225 through 230 Processing helix chain '1' and resid 230 through 238 Processing helix chain '1' and resid 238 through 243 Processing helix chain '1' and resid 275 through 284 Processing helix chain '1' and resid 290 through 292 No H-bonds generated for 'chain '1' and resid 290 through 292' Processing helix chain '1' and resid 309 through 313 Processing helix chain '1' and resid 318 through 325 removed outlier: 3.519A pdb=" N LEU 1 322 " --> pdb=" O ASP 1 318 " (cutoff:3.500A) Processing helix chain '1' and resid 342 through 357 Processing helix chain '1' and resid 362 through 382 removed outlier: 4.483A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 400 removed outlier: 4.199A pdb=" N ASP 1 390 " --> pdb=" O PRO 1 386 " (cutoff:3.500A) Processing helix chain '1' and resid 406 through 438 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 24 through 36 Processing helix chain '2' and resid 42 through 45 Processing helix chain '2' and resid 46 through 59 Processing helix chain '2' and resid 64 through 74 Processing helix chain '2' and resid 76 through 87 removed outlier: 3.557A pdb=" N VAL 2 80 " --> pdb=" O PRO 2 76 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 105 through 111 removed outlier: 3.739A pdb=" N ARG 2 111 " --> pdb=" O PRO 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 112 through 125 removed outlier: 4.153A pdb=" N ILE 2 116 " --> pdb=" O ASN 2 112 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 151 Processing helix chain '2' and resid 165 through 178 Processing helix chain '3' and resid 25 through 32 Processing helix chain '3' and resid 83 through 100 removed outlier: 4.446A pdb=" N ASN 3 100 " --> pdb=" O PHE 3 96 " (cutoff:3.500A) Processing helix chain '3' and resid 114 through 124 Processing helix chain '3' and resid 150 through 153 Processing helix chain '3' and resid 157 through 166 Processing helix chain '3' and resid 177 through 181 removed outlier: 3.553A pdb=" N ASP 3 180 " --> pdb=" O ARG 3 177 " (cutoff:3.500A) Processing helix chain '3' and resid 197 through 203 removed outlier: 3.827A pdb=" N ASP 3 201 " --> pdb=" O GLY 3 197 " (cutoff:3.500A) Processing helix chain '3' and resid 218 through 222 Processing helix chain '3' and resid 264 through 270 Processing helix chain '3' and resid 271 through 276 removed outlier: 3.575A pdb=" N LYS 3 275 " --> pdb=" O ASP 3 272 " (cutoff:3.500A) Processing helix chain '3' and resid 295 through 308 removed outlier: 3.713A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 311 through 313 No H-bonds generated for 'chain '3' and resid 311 through 313' Processing helix chain '3' and resid 324 through 338 removed outlier: 3.574A pdb=" N VAL 3 338 " --> pdb=" O LEU 3 334 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 363 removed outlier: 3.721A pdb=" N LEU 3 363 " --> pdb=" O SER 3 360 " (cutoff:3.500A) Processing helix chain '3' and resid 368 through 374 Processing helix chain '3' and resid 383 through 388 Processing helix chain '3' and resid 388 through 403 removed outlier: 3.553A pdb=" N ASP 3 403 " --> pdb=" O TRP 3 399 " (cutoff:3.500A) Processing helix chain '3' and resid 426 through 433 removed outlier: 3.819A pdb=" N GLN 3 430 " --> pdb=" O PRO 3 426 " (cutoff:3.500A) Processing helix chain '3' and resid 437 through 446 removed outlier: 4.194A pdb=" N GLN 3 441 " --> pdb=" O HIS 3 437 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 456 through 460 removed outlier: 3.584A pdb=" N ARG 3 460 " --> pdb=" O ALA 3 457 " (cutoff:3.500A) Processing helix chain '3' and resid 462 through 479 Processing helix chain '3' and resid 498 through 505 Processing helix chain '3' and resid 511 through 517 removed outlier: 3.880A pdb=" N ASN 3 517 " --> pdb=" O ALA 3 513 " (cutoff:3.500A) Processing helix chain '3' and resid 565 through 569 removed outlier: 4.029A pdb=" N LYS 3 569 " --> pdb=" O TYR 3 566 " (cutoff:3.500A) Processing helix chain '3' and resid 595 through 607 Processing helix chain '3' and resid 615 through 627 Processing helix chain '3' and resid 628 through 632 removed outlier: 3.909A pdb=" N VAL 3 631 " --> pdb=" O PRO 3 628 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG 3 632 " --> pdb=" O ASN 3 629 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 628 through 632' Processing helix chain '3' and resid 641 through 650 Processing helix chain '3' and resid 667 through 671 Processing helix chain '3' and resid 675 through 680 Processing helix chain '3' and resid 681 through 693 Processing helix chain '4' and resid 86 through 91 Processing helix chain '4' and resid 92 through 94 No H-bonds generated for 'chain '4' and resid 92 through 94' Processing helix chain '4' and resid 95 through 100 Processing helix chain '4' and resid 100 through 105 removed outlier: 3.913A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG 4 105 " --> pdb=" O PRO 4 101 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 100 through 105' Processing helix chain '4' and resid 110 through 127 Processing helix chain '4' and resid 131 through 162 removed outlier: 3.535A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 164 through 186 removed outlier: 3.922A pdb=" N PHE 4 168 " --> pdb=" O MET 4 164 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 206 through 230 removed outlier: 3.870A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 232 through 238 Processing helix chain '4' and resid 246 through 253 Processing helix chain '4' and resid 257 through 262 Processing helix chain '4' and resid 268 through 273 Processing helix chain '4' and resid 292 through 317 Processing helix chain '4' and resid 334 through 339 Processing helix chain '4' and resid 341 through 354 Processing helix chain '4' and resid 393 through 406 removed outlier: 4.190A pdb=" N ALA 4 397 " --> pdb=" O ALA 4 393 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 410 through 421 removed outlier: 4.038A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 424 through 430 Processing helix chain '5' and resid 15 through 33 Processing helix chain '5' and resid 56 through 67 Processing helix chain '5' and resid 126 through 139 removed outlier: 4.150A pdb=" N TYR 5 130 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG 5 132 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) Processing helix chain '5' and resid 206 through 210 Processing helix chain '6' and resid 25 through 44 Processing helix chain '6' and resid 53 through 64 removed outlier: 4.094A pdb=" N VAL 6 57 " --> pdb=" O ALA 6 53 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU 6 58 " --> pdb=" O CYS 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 68 through 73 Processing helix chain '6' and resid 96 through 107 Processing helix chain '6' and resid 117 through 123 Processing helix chain '6' and resid 124 through 127 Processing helix chain '6' and resid 135 through 139 Processing helix chain '6' and resid 152 through 169 Processing helix chain '6' and resid 171 through 179 Processing helix chain '9' and resid 13 through 27 Processing helix chain '9' and resid 27 through 42 Processing helix chain '9' and resid 81 through 87 Processing helix chain '9' and resid 120 through 126 Processing helix chain '9' and resid 143 through 146 Processing helix chain '9' and resid 150 through 173 removed outlier: 5.856A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) Processing helix chain '9' and resid 174 through 176 No H-bonds generated for 'chain '9' and resid 174 through 176' Processing helix chain 'a' and resid 41 through 46 removed outlier: 3.629A pdb=" N HIS a 44 " --> pdb=" O LEU a 41 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR a 46 " --> pdb=" O HIS a 43 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 59 Processing helix chain 'a' and resid 60 through 62 No H-bonds generated for 'chain 'a' and resid 60 through 62' Processing helix chain 'b' and resid 22 through 29 removed outlier: 3.668A pdb=" N ARG b 25 " --> pdb=" O ASP b 22 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 46 removed outlier: 3.657A pdb=" N ALA b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 63 through 67 Processing helix chain 'c' and resid 27 through 32 removed outlier: 3.568A pdb=" N THR c 32 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 53 removed outlier: 3.918A pdb=" N LYS c 53 " --> pdb=" O ASN c 50 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 82 removed outlier: 3.593A pdb=" N SER c 80 " --> pdb=" O ASP c 77 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 99 removed outlier: 3.514A pdb=" N ALA c 92 " --> pdb=" O THR c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 117 through 123 removed outlier: 3.717A pdb=" N SER c 123 " --> pdb=" O ALA c 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE d 6 " --> pdb=" O HIS d 3 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 40 removed outlier: 3.919A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 63 removed outlier: 5.150A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 77 through 86 Processing helix chain 'd' and resid 105 through 111 Processing helix chain 'd' and resid 111 through 124 Processing helix chain 'd' and resid 143 through 160 Processing helix chain 'd' and resid 178 through 184 Processing helix chain 'd' and resid 207 through 220 Processing helix chain 'd' and resid 221 through 224 removed outlier: 3.691A pdb=" N ARG d 224 " --> pdb=" O PRO d 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 221 through 224' Processing helix chain 'd' and resid 238 through 249 Processing helix chain 'd' and resid 280 through 288 Processing helix chain 'd' and resid 300 through 304 Processing helix chain 'd' and resid 309 through 319 removed outlier: 3.866A pdb=" N LYS d 313 " --> pdb=" O PRO d 309 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 26 through 28 No H-bonds generated for 'chain 'e' and resid 26 through 28' Processing helix chain 'e' and resid 29 through 47 removed outlier: 3.770A pdb=" N LYS e 38 " --> pdb=" O ASP e 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR e 40 " --> pdb=" O ILE e 36 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL e 41 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU e 42 " --> pdb=" O LYS e 38 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU e 43 " --> pdb=" O ARG e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 97 removed outlier: 3.707A pdb=" N LYS e 97 " --> pdb=" O VAL e 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 35 Processing helix chain 'f' and resid 41 through 61 Processing helix chain 'f' and resid 63 through 72 Processing helix chain 'f' and resid 75 through 97 removed outlier: 3.811A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 23 through 49 removed outlier: 3.607A pdb=" N ALA g 27 " --> pdb=" O ASP g 23 " (cutoff:3.500A) Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 54 through 69 removed outlier: 3.956A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 94 Processing helix chain 'g' and resid 98 through 104 Processing helix chain 'g' and resid 116 through 124 removed outlier: 3.536A pdb=" N LYS g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 16 Processing helix chain 'h' and resid 52 through 56 Processing helix chain 'i' and resid 2 through 17 Processing helix chain 'i' and resid 19 through 31 Processing helix chain 'i' and resid 78 through 82 removed outlier: 3.668A pdb=" N VAL i 82 " --> pdb=" O GLY i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 83 through 91 removed outlier: 3.631A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 22 Processing helix chain 'j' and resid 43 through 59 Processing helix chain 'j' and resid 72 through 83 Processing helix chain 'q' and resid 30 through 35 removed outlier: 3.677A pdb=" N PHE q 35 " --> pdb=" O GLY q 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 174 through 179 removed outlier: 6.062A pdb=" N ALA 1 134 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL 1 178 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE 1 136 " --> pdb=" O VAL 1 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 266 through 271 Processing sheet with id=AA3, first strand: chain '2' and resid 137 through 142 removed outlier: 6.542A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 16 through 20 removed outlier: 9.068A pdb=" N ILE 3 79 " --> pdb=" O GLU 3 10 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE 3 12 " --> pdb=" O ILE 3 79 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU 3 58 " --> pdb=" O LEU 3 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 146 through 148 Processing sheet with id=AA6, first strand: chain '3' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain '3' and resid 223 through 228 Processing sheet with id=AA8, first strand: chain '3' and resid 291 through 293 removed outlier: 6.656A pdb=" N ILE 3 543 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU 3 561 " --> pdb=" O ILE 3 543 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR 3 545 " --> pdb=" O LEU 3 561 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 420 through 423 removed outlier: 7.011A pdb=" N VAL 3 406 " --> pdb=" O ASP 3 420 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU 3 422 " --> pdb=" O VAL 3 406 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU 3 408 " --> pdb=" O LEU 3 422 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 572 through 574 Processing sheet with id=AB2, first strand: chain '4' and resid 47 through 51 removed outlier: 6.631A pdb=" N ARG 4 63 " --> pdb=" O PRO 4 78 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL 4 65 " --> pdb=" O CYS 4 76 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS 4 76 " --> pdb=" O VAL 4 65 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU 4 67 " --> pdb=" O ARG 4 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '4' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain '4' and resid 285 through 287 Processing sheet with id=AB5, first strand: chain '4' and resid 361 through 369 Processing sheet with id=AB6, first strand: chain '5' and resid 74 through 82 removed outlier: 5.375A pdb=" N LEU 5 75 " --> pdb=" O LEU 5 97 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU 5 97 " --> pdb=" O LEU 5 75 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 104 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU 5 49 " --> pdb=" O VAL 5 40 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL 5 40 " --> pdb=" O GLU 5 49 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS 5 51 " --> pdb=" O GLN 5 38 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL 5 42 " --> pdb=" O ILE h 67 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE h 67 " --> pdb=" O VAL 5 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 117 through 118 removed outlier: 6.618A pdb=" N VAL 5 117 " --> pdb=" O ALA 5 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '5' and resid 172 through 177 Processing sheet with id=AB9, first strand: chain '6' and resid 47 through 51 removed outlier: 6.819A pdb=" N VAL 6 113 " --> pdb=" O ILE 6 144 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL 6 146 " --> pdb=" O VAL 6 113 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER 6 115 " --> pdb=" O VAL 6 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '9' and resid 65 through 67 Processing sheet with id=AC2, first strand: chain '9' and resid 92 through 98 removed outlier: 6.367A pdb=" N THR 9 93 " --> pdb=" O TYR 9 109 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR 9 109 " --> pdb=" O THR 9 93 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLU 9 95 " --> pdb=" O THR 9 107 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG 9 105 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 3 through 4 removed outlier: 4.395A pdb=" N ARG b 3 " --> pdb=" O VAL b 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 50 through 52 removed outlier: 6.083A pdb=" N SER b 50 " --> pdb=" O ARG b 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 56 through 59 Processing sheet with id=AC6, first strand: chain 'c' and resid 11 through 12 Processing sheet with id=AC7, first strand: chain 'c' and resid 84 through 86 Processing sheet with id=AC8, first strand: chain 'c' and resid 64 through 66 Processing sheet with id=AC9, first strand: chain 'd' and resid 68 through 72 removed outlier: 6.430A pdb=" N ALA d 21 " --> pdb=" O ILE d 46 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL d 23 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL d 91 " --> pdb=" O ILE d 130 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE d 132 " --> pdb=" O VAL d 91 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASN d 93 " --> pdb=" O ILE d 132 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 171 through 172 Processing sheet with id=AD2, first strand: chain 'd' and resid 201 through 202 Processing sheet with id=AD3, first strand: chain 'e' and resid 52 through 57 removed outlier: 8.552A pdb=" N LEU e 53 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE e 18 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ARG e 55 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE e 20 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N CYS e 57 " --> pdb=" O ILE e 20 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU e 22 " --> pdb=" O CYS e 57 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'i' and resid 37 through 41 removed outlier: 5.578A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'i' and resid 67 through 68 1122 hydrogen bonds defined for protein. 3108 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: 5.77 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 12001 1.43 - 1.67: 16418 1.67 - 1.90: 255 1.90 - 2.14: 0 2.14 - 2.37: 80 Bond restraints: 28754 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.591 0.242 3.80e-02 6.93e+02 4.05e+01 bond pdb=" O5D NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 1.757 1.565 0.192 3.50e-02 8.16e+02 3.01e+01 bond pdb=" C4 FMN 1 502 " pdb=" C4A FMN 1 502 " ideal model delta sigma weight residual 1.485 1.379 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O5 ZMP g 201 " pdb=" P1 ZMP g 201 " ideal model delta sigma weight residual 1.715 1.610 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O7 ZMP g 201 " pdb=" P1 ZMP g 201 " ideal model delta sigma weight residual 1.528 1.606 -0.078 2.00e-02 2.50e+03 1.54e+01 ... (remaining 28749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.35: 38882 9.35 - 18.69: 32 18.69 - 28.04: 3 28.04 - 37.39: 0 37.39 - 46.74: 2 Bond angle restraints: 38919 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 73.86 46.74 3.00e+00 1.11e-01 2.43e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 70.25 39.05 3.00e+00 1.11e-01 1.69e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.45 -23.71 1.95e+00 2.62e-01 1.47e+02 angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.90 13.43 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.85 13.48 1.20e+00 6.94e-01 1.26e+02 ... (remaining 38914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.77: 17248 30.77 - 61.54: 249 61.54 - 92.31: 23 92.31 - 123.09: 3 123.09 - 153.86: 2 Dihedral angle restraints: 17525 sinusoidal: 7479 harmonic: 10046 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual -180.00 -130.85 -49.15 0 5.00e+00 4.00e-02 9.66e+01 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -135.06 -44.94 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA THR 3 366 " pdb=" C THR 3 366 " pdb=" N THR 3 367 " pdb=" CA THR 3 367 " ideal model delta harmonic sigma weight residual 180.00 147.11 32.89 0 5.00e+00 4.00e-02 4.33e+01 ... (remaining 17522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.237: 4192 4.237 - 8.475: 0 8.475 - 12.712: 0 12.712 - 16.950: 0 16.950 - 21.187: 24 Chirality restraints: 4216 Sorted by residual: chirality pdb="FE1 SF4 9 403 " pdb=" S2 SF4 9 403 " pdb=" S3 SF4 9 403 " pdb=" S4 SF4 9 403 " both_signs ideal model delta sigma weight residual False -10.55 10.63 -21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 9 402 " pdb=" S1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S3 SF4 9 402 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 4213 not shown) Planarity restraints: 4995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.039 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR 6 125 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.019 2.00e-02 2.50e+03 3.32e-02 2.20e+01 pdb=" CG TYR 9 40 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 1 371 " 0.026 2.00e-02 2.50e+03 2.46e-02 1.51e+01 pdb=" CG TRP 1 371 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP 1 371 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP 1 371 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP 1 371 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP 1 371 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP 1 371 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP 1 371 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP 1 371 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP 1 371 " 0.001 2.00e-02 2.50e+03 ... (remaining 4992 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.83: 10115 2.83 - 3.41: 33545 3.41 - 3.99: 68815 3.99 - 4.56: 92266 4.56 - 5.14: 131117 Nonbonded interactions: 335858 Sorted by model distance: nonbonded pdb=" OD2 ASP 5 77 " pdb=" OG1 THR 5 79 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR d 33 " pdb=" O HOH d 501 " model vdw 2.260 3.040 nonbonded pdb=" O PHE 4 141 " pdb=" OG1 THR 4 145 " model vdw 2.269 3.040 nonbonded pdb=" O ILE 9 94 " pdb=" O HOH 9 501 " model vdw 2.276 3.040 nonbonded pdb=" OG SER 5 119 " pdb=" OE2 GLU 5 131 " model vdw 2.278 3.040 ... (remaining 335853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 32.240 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 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 : 0.013 0.768 28790 Z= 0.461 Angle : 1.122 46.737 39003 Z= 0.574 Chirality : 1.582 21.187 4216 Planarity : 0.008 0.062 4995 Dihedral : 10.984 153.858 11061 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.12), residues: 3430 helix: -2.26 (0.10), residues: 1325 sheet: -1.27 (0.23), residues: 366 loop : -1.15 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 3 579 TYR 0.085 0.004 TYR 6 125 PHE 0.060 0.004 PHE 4 171 TRP 0.064 0.004 TRP 1 371 HIS 0.018 0.003 HIS 4 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.34 (28754) covalent geometry : angle 1.06197 / 0.57 (38919) hydrogen bonds : bond 0.15380 / 10.12 ( 1122) hydrogen bonds : angle 7.40966 / 5.16 ( 3108) metal coordination : bond 0.30240 / 17.72 ( 36) metal coordination : angle 7.84750 / 5.23 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 639 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 428 GLU cc_start: 0.8910 (pp20) cc_final: 0.8426 (pp20) REVERT: 1 432 ARG cc_start: 0.8291 (ptt-90) cc_final: 0.8067 (ttp-110) REVERT: 1 435 GLN cc_start: 0.8779 (pp30) cc_final: 0.8499 (pt0) REVERT: 1 437 HIS cc_start: 0.7412 (m-70) cc_final: 0.7162 (m90) REVERT: 2 180 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8227 (mttp) REVERT: 3 31 GLU cc_start: 0.9035 (tt0) cc_final: 0.8590 (tt0) REVERT: 3 141 ASN cc_start: 0.8639 (t0) cc_final: 0.8328 (t0) REVERT: 3 337 ARG cc_start: 0.8785 (mmt-90) cc_final: 0.8542 (mmt90) REVERT: 3 640 ASN cc_start: 0.9070 (t0) cc_final: 0.8664 (t0) REVERT: 4 282 GLU cc_start: 0.8688 (tt0) cc_final: 0.8455 (tt0) REVERT: 5 158 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8585 (mt-10) REVERT: 6 25 ARG cc_start: 0.7964 (ttt180) cc_final: 0.7744 (tpt170) REVERT: 6 81 ARG cc_start: 0.8732 (mtp180) cc_final: 0.7505 (tpt90) REVERT: 6 102 LYS cc_start: 0.9205 (tttt) cc_final: 0.8960 (tttm) REVERT: 9 81 LYS cc_start: 0.8751 (mttp) cc_final: 0.8478 (mttm) REVERT: a 71 GLU cc_start: 0.8731 (tt0) cc_final: 0.8513 (tp30) REVERT: b 10 LYS cc_start: 0.8980 (mtmp) cc_final: 0.8755 (mtpp) REVERT: b 21 GLU cc_start: 0.9020 (pm20) cc_final: 0.8794 (pm20) REVERT: c 18 ASP cc_start: 0.8966 (t70) cc_final: 0.8748 (t0) REVERT: c 90 GLU cc_start: 0.9205 (mp0) cc_final: 0.8968 (mp0) REVERT: c 97 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8821 (mt-10) REVERT: d 107 GLU cc_start: 0.8930 (tt0) cc_final: 0.8724 (tm-30) REVERT: d 162 GLU cc_start: 0.8998 (mp0) cc_final: 0.8754 (mp0) REVERT: d 224 ARG cc_start: 0.8680 (mtp85) cc_final: 0.8273 (mmp80) REVERT: f 6 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8602 (ttpt) REVERT: f 39 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8436 (mppt) REVERT: h 17 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7651 (mmt-90) REVERT: h 71 SER cc_start: 0.8676 (m) cc_final: 0.8431 (p) REVERT: i 8 LYS cc_start: 0.8859 (mttt) cc_final: 0.8034 (mmtt) REVERT: i 21 ARG cc_start: 0.8773 (ttm-80) cc_final: 0.8235 (mpt180) REVERT: i 50 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8330 (mt-10) REVERT: i 101 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8796 (mtpp) REVERT: i 114 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8562 (mttp) REVERT: j 71 MET cc_start: 0.8829 (mmp) cc_final: 0.8447 (mmp) REVERT: j 74 GLN cc_start: 0.9058 (tp40) cc_final: 0.8547 (tp40) REVERT: j 77 VAL cc_start: 0.9313 (p) cc_final: 0.9039 (m) REVERT: j 78 ASP cc_start: 0.8983 (m-30) cc_final: 0.8737 (m-30) outliers start: 2 outliers final: 5 residues processed: 641 average time/residue: 0.8434 time to fit residues: 614.4027 Evaluate side-chains 465 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 460 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 596 ASP Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain j residue 39 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 148 ASN 1 356 HIS 1 373 ASN 3 179 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 277 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 665 GLN ** 4 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 232 ASN 4 252 ASN 4 313 GLN 5 211 GLN 6 106 GLN 6 162 GLN 9 6 ASN 9 65 HIS a 35 ASN a 40 ASN a 55 ASN b 36 ASN b 74 ASN c 67 ASN d 115 GLN d 184 ASN e 30 GLN e 47 ASN e 92 ASN f 49 GLN f 75 GLN f 95 GLN g 125 HIS h 28 GLN i 69 ASN i 122 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.076389 restraints weight = 24893.786| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.09 r_work: 0.2861 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9238 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.258 28790 Z= 0.415 Angle : 2.667 50.668 39003 Z= 1.536 Chirality : 0.484 6.600 4216 Planarity : 0.005 0.047 4995 Dihedral : 9.798 159.958 4210 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.27 % Allowed : 8.04 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3430 helix: -0.45 (0.13), residues: 1327 sheet: -1.08 (0.24), residues: 366 loop : -0.57 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 3 127 TYR 0.029 0.002 TYR 9 40 PHE 0.026 0.002 PHE 4 171 TRP 0.030 0.001 TRP 1 371 HIS 0.006 0.001 HIS 3 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01204 / 0.41 (28754) covalent geometry : angle 2.32800 / 1.53 (38919) hydrogen bonds : bond 0.04217 / 2.79 ( 1122) hydrogen bonds : angle 5.49931 / 3.83 ( 3108) metal coordination : bond 0.04854 / 2.85 ( 36) metal coordination : angle 28.13931 / 17.60 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 480 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 431 GLN cc_start: 0.8330 (pp30) cc_final: 0.8121 (pp30) REVERT: 2 180 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8326 (mttp) REVERT: 3 31 GLU cc_start: 0.8556 (tt0) cc_final: 0.8198 (tt0) REVERT: 3 588 MET cc_start: 0.9232 (mmt) cc_final: 0.9011 (mmt) REVERT: 3 640 ASN cc_start: 0.8708 (t0) cc_final: 0.8465 (t160) REVERT: 4 74 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7970 (mmt90) REVERT: 6 48 MET cc_start: 0.8558 (tmt) cc_final: 0.8296 (tmt) REVERT: 6 81 ARG cc_start: 0.8505 (mtp180) cc_final: 0.7699 (tpt90) REVERT: 6 102 LYS cc_start: 0.9222 (tttt) cc_final: 0.9019 (tttm) REVERT: 6 174 ARG cc_start: 0.8604 (mtm-85) cc_final: 0.8325 (mtt180) REVERT: d 320 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7718 (ttm170) REVERT: e 30 GLN cc_start: 0.8997 (tp40) cc_final: 0.8696 (tp-100) REVERT: e 39 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7818 (mtm-85) REVERT: f 39 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8477 (mppt) REVERT: g 17 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8618 (tttt) REVERT: h 17 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7812 (mmt-90) REVERT: h 47 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7855 (mtm-85) REVERT: h 108 ASP cc_start: 0.8740 (t70) cc_final: 0.8525 (t0) REVERT: i 8 LYS cc_start: 0.8716 (mttt) cc_final: 0.8173 (mptt) REVERT: i 50 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8257 (mt-10) REVERT: i 71 LYS cc_start: 0.9156 (ttmm) cc_final: 0.8943 (tttm) REVERT: j 74 GLN cc_start: 0.9088 (tp40) cc_final: 0.8650 (tp40) REVERT: j 78 ASP cc_start: 0.8875 (m-30) cc_final: 0.8555 (m-30) outliers start: 38 outliers final: 6 residues processed: 495 average time/residue: 0.8244 time to fit residues: 464.5875 Evaluate side-chains 438 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 429 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 74 ARG Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain d residue 320 ARG Chi-restraints excluded: chain e residue 39 ARG Chi-restraints excluded: chain e residue 49 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 225 optimal weight: 20.0000 chunk 110 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 361 GLN 1 437 HIS ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 444 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN ** b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 74 ASN d 184 ASN d 234 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 123 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.073743 restraints weight = 24644.228| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.08 r_work: 0.2804 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 28790 Z= 0.427 Angle : 2.663 50.608 39003 Z= 1.535 Chirality : 0.485 6.593 4216 Planarity : 0.005 0.047 4995 Dihedral : 9.525 158.862 4203 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.94 % Allowed : 8.95 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3430 helix: 0.32 (0.14), residues: 1337 sheet: -0.78 (0.25), residues: 364 loop : -0.24 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 224 TYR 0.023 0.002 TYR 9 118 PHE 0.028 0.002 PHE 4 171 TRP 0.021 0.001 TRP 1 371 HIS 0.009 0.002 HIS 4 150 Details of bonding type rmsd/Z covalent geometry : bond 0.01227 / 0.43 (28754) covalent geometry : angle 2.32679 / 1.53 (38919) hydrogen bonds : bond 0.04108 / 2.71 ( 1122) hydrogen bonds : angle 5.23193 / 3.63 ( 3108) metal coordination : bond 0.04292 / 2.57 ( 36) metal coordination : angle 27.99835 / 17.50 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 431 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: 2 180 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8314 (mttp) REVERT: 3 31 GLU cc_start: 0.8599 (tt0) cc_final: 0.8212 (tt0) REVERT: 3 588 MET cc_start: 0.9257 (mmt) cc_final: 0.9018 (mmt) REVERT: 3 640 ASN cc_start: 0.8703 (t0) cc_final: 0.8379 (t160) REVERT: 5 125 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8965 (mtpp) REVERT: 6 81 ARG cc_start: 0.8559 (mtp180) cc_final: 0.7693 (tpt90) REVERT: 6 102 LYS cc_start: 0.9252 (tttt) cc_final: 0.9039 (tttm) REVERT: 6 174 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8261 (mpt-90) REVERT: 9 15 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8223 (tptm) REVERT: c 28 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: d 320 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7809 (ttm170) REVERT: e 30 GLN cc_start: 0.9114 (tp40) cc_final: 0.8825 (tp-100) REVERT: e 39 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8228 (mtm-85) REVERT: f 39 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8503 (mppt) REVERT: h 17 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7780 (mmt-90) REVERT: h 47 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7908 (mtm-85) REVERT: h 108 ASP cc_start: 0.8710 (t70) cc_final: 0.8486 (t0) REVERT: i 8 LYS cc_start: 0.8722 (mttt) cc_final: 0.8276 (mptt) REVERT: i 50 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8103 (tt0) REVERT: q 26 ARG cc_start: 0.7816 (tmm160) cc_final: 0.7373 (tmm160) outliers start: 58 outliers final: 16 residues processed: 458 average time/residue: 0.8063 time to fit residues: 421.6985 Evaluate side-chains 444 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 423 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 135 ARG Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 390 LEU Chi-restraints excluded: chain 3 residue 646 SER Chi-restraints excluded: chain 3 residue 657 LEU Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 5 residue 125 LYS Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 9 residue 15 LYS Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain d residue 185 ILE Chi-restraints excluded: chain d residue 320 ARG Chi-restraints excluded: chain e residue 39 ARG Chi-restraints excluded: chain e residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 84 optimal weight: 5.9990 chunk 336 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 323 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 398 GLN 1 437 HIS ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 444 GLN 3 459 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 144 ASN 5 211 GLN 6 162 GLN a 35 ASN a 40 ASN ** b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 184 ASN d 234 ASN e 85 GLN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN i 123 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.073574 restraints weight = 23948.074| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.07 r_work: 0.2801 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 28790 Z= 0.421 Angle : 2.662 50.623 39003 Z= 1.534 Chirality : 0.484 6.555 4216 Planarity : 0.005 0.045 4995 Dihedral : 9.232 158.867 4201 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 9.88 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3430 helix: 0.68 (0.14), residues: 1340 sheet: -0.71 (0.25), residues: 353 loop : -0.04 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 5 14 TYR 0.021 0.002 TYR 9 118 PHE 0.022 0.002 PHE 4 171 TRP 0.015 0.001 TRP 1 371 HIS 0.008 0.001 HIS 4 150 Details of bonding type rmsd/Z covalent geometry : bond 0.01218 / 0.42 (28754) covalent geometry : angle 2.32351 / 1.53 (38919) hydrogen bonds : bond 0.03914 / 2.58 ( 1122) hydrogen bonds : angle 5.09434 / 3.53 ( 3108) metal coordination : bond 0.03705 / 2.18 ( 36) metal coordination : angle 28.10976 / 17.53 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 426 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: 1 428 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8415 (tm-30) REVERT: 1 431 GLN cc_start: 0.8479 (pp30) cc_final: 0.8214 (pp30) REVERT: 2 180 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8300 (mttp) REVERT: 3 31 GLU cc_start: 0.8579 (tt0) cc_final: 0.8086 (tt0) REVERT: 3 640 ASN cc_start: 0.8692 (t0) cc_final: 0.8385 (t0) REVERT: 6 81 ARG cc_start: 0.8574 (mtp180) cc_final: 0.7687 (tpt90) REVERT: 6 102 LYS cc_start: 0.9255 (tttt) cc_final: 0.9038 (tttm) REVERT: 6 174 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8274 (mpt-90) REVERT: c 28 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: d 52 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: d 320 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7897 (ttm170) REVERT: e 30 GLN cc_start: 0.9104 (tp40) cc_final: 0.8889 (tp-100) REVERT: e 39 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8082 (mtm-85) REVERT: f 39 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8492 (mppt) REVERT: g 26 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: g 98 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8124 (mp10) REVERT: h 17 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7743 (mmt-90) REVERT: h 47 ARG cc_start: 0.8275 (mtm110) cc_final: 0.7937 (mtm-85) REVERT: h 108 ASP cc_start: 0.8684 (t70) cc_final: 0.8471 (t0) REVERT: i 8 LYS cc_start: 0.8754 (mttt) cc_final: 0.8278 (mptt) REVERT: i 50 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8141 (tt0) REVERT: q 26 ARG cc_start: 0.7863 (tmm160) cc_final: 0.7393 (tmm160) outliers start: 64 outliers final: 20 residues processed: 458 average time/residue: 0.8029 time to fit residues: 420.8453 Evaluate side-chains 440 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 413 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 326 GLN Chi-restraints excluded: chain 1 residue 428 GLU Chi-restraints excluded: chain 3 residue 135 ARG Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 390 LEU Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 646 SER Chi-restraints excluded: chain 3 residue 657 LEU Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 282 GLU Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 79 SER Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 320 ARG Chi-restraints excluded: chain e residue 39 ARG Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 69 GLU Chi-restraints excluded: chain g residue 26 GLU Chi-restraints excluded: chain g residue 98 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 7.9990 chunk 324 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 265 optimal weight: 0.7980 chunk 281 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 373 ASN 3 16 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 444 GLN 3 461 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN d 296 HIS e 47 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN i 123 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.072171 restraints weight = 23902.847| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.06 r_work: 0.2772 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9296 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.240 28790 Z= 0.437 Angle : 2.666 50.671 39003 Z= 1.537 Chirality : 0.485 6.615 4216 Planarity : 0.005 0.057 4995 Dihedral : 9.219 158.816 4201 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.14 % Allowed : 10.45 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3430 helix: 0.78 (0.14), residues: 1344 sheet: -0.61 (0.25), residues: 355 loop : 0.02 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 339 TYR 0.022 0.002 TYR 9 118 PHE 0.021 0.002 PHE 4 171 TRP 0.012 0.001 TRP 1 371 HIS 0.008 0.002 HIS 4 150 Details of bonding type rmsd/Z covalent geometry : bond 0.01244 / 0.44 (28754) covalent geometry : angle 2.33025 / 1.53 (38919) hydrogen bonds : bond 0.04155 / 2.73 ( 1122) hydrogen bonds : angle 5.13279 / 3.56 ( 3108) metal coordination : bond 0.04199 / 2.50 ( 36) metal coordination : angle 28.02355 / 17.48 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 428 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: 1 428 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: 1 431 GLN cc_start: 0.8504 (pp30) cc_final: 0.8221 (pp30) REVERT: 2 180 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8309 (mttp) REVERT: 3 640 ASN cc_start: 0.8699 (t0) cc_final: 0.8382 (t0) REVERT: 4 410 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7340 (mmt) REVERT: 6 81 ARG cc_start: 0.8601 (mtp180) cc_final: 0.7716 (tpt90) REVERT: 6 102 LYS cc_start: 0.9269 (tttt) cc_final: 0.9054 (tttm) REVERT: 6 174 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8289 (mpt-90) REVERT: 9 15 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8478 (tptp) REVERT: c 28 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: d 52 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: d 320 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7930 (ttm170) REVERT: e 30 GLN cc_start: 0.9133 (tp40) cc_final: 0.8911 (tp-100) REVERT: e 39 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8105 (mtm-85) REVERT: f 29 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8792 (mtpt) REVERT: f 39 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8480 (mppt) REVERT: g 98 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: h 17 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7741 (mmt-90) REVERT: i 8 LYS cc_start: 0.8773 (mttt) cc_final: 0.8287 (mptt) REVERT: i 50 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8125 (tt0) REVERT: q 21 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8122 (mmtm) REVERT: q 26 ARG cc_start: 0.7879 (tmm160) cc_final: 0.7452 (tmm160) outliers start: 64 outliers final: 25 residues processed: 456 average time/residue: 0.8261 time to fit residues: 430.0464 Evaluate side-chains 453 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 418 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 248 GLU Chi-restraints excluded: chain 1 residue 326 GLN Chi-restraints excluded: chain 1 residue 428 GLU Chi-restraints excluded: chain 3 residue 135 ARG Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 390 LEU Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 646 SER Chi-restraints excluded: chain 3 residue 657 LEU Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 282 GLU Chi-restraints excluded: chain 4 residue 410 MET Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 79 SER Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 15 LYS Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 320 ARG Chi-restraints excluded: chain e residue 17 GLU Chi-restraints excluded: chain e residue 39 ARG Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 69 GLU Chi-restraints excluded: chain g residue 25 ASN Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain q residue 21 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 314 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 437 HIS 3 461 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN e 47 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN h 28 GLN i 12 GLN i 123 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.072435 restraints weight = 23725.052| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.06 r_work: 0.2777 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9291 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 28790 Z= 0.429 Angle : 2.664 50.653 39003 Z= 1.535 Chirality : 0.485 6.586 4216 Planarity : 0.005 0.052 4995 Dihedral : 9.158 158.851 4201 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.10 % Allowed : 10.85 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3430 helix: 0.88 (0.14), residues: 1343 sheet: -0.59 (0.25), residues: 355 loop : 0.06 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 1 339 TYR 0.021 0.002 TYR 9 118 PHE 0.019 0.002 PHE i 55 TRP 0.011 0.001 TRP 5 203 HIS 0.007 0.001 HIS 5 160 Details of bonding type rmsd/Z covalent geometry : bond 0.01231 / 0.43 (28754) covalent geometry : angle 2.32608 / 1.53 (38919) hydrogen bonds : bond 0.04020 / 2.65 ( 1122) hydrogen bonds : angle 5.09502 / 3.54 ( 3108) metal coordination : bond 0.03915 / 2.32 ( 36) metal coordination : angle 28.07949 / 17.49 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 425 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: 1 428 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8390 (pp20) REVERT: 1 431 GLN cc_start: 0.8504 (pp30) cc_final: 0.8137 (pp30) REVERT: 2 180 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8313 (mttp) REVERT: 3 246 GLU cc_start: 0.8557 (tt0) cc_final: 0.8328 (tt0) REVERT: 3 640 ASN cc_start: 0.8708 (t0) cc_final: 0.8396 (t0) REVERT: 4 410 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7288 (mmt) REVERT: 6 81 ARG cc_start: 0.8611 (mtp180) cc_final: 0.7739 (tpt90) REVERT: 6 102 LYS cc_start: 0.9276 (tttt) cc_final: 0.9064 (tttm) REVERT: 6 174 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8291 (mpt-90) REVERT: c 28 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: d 52 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: d 320 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7983 (ttm170) REVERT: e 30 GLN cc_start: 0.9129 (tp40) cc_final: 0.8839 (tp-100) REVERT: f 29 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8785 (mtpt) REVERT: f 39 LYS cc_start: 0.8726 (mtmm) cc_final: 0.8465 (mppt) REVERT: g 26 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8092 (pt0) REVERT: g 98 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: h 17 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7727 (mmt-90) REVERT: i 8 LYS cc_start: 0.8776 (mttt) cc_final: 0.8288 (mptt) REVERT: i 50 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8110 (tt0) REVERT: q 26 ARG cc_start: 0.7875 (tmm160) cc_final: 0.7481 (tmm160) outliers start: 63 outliers final: 29 residues processed: 454 average time/residue: 0.8310 time to fit residues: 430.9454 Evaluate side-chains 456 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 420 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 248 GLU Chi-restraints excluded: chain 1 residue 324 GLN Chi-restraints excluded: chain 1 residue 428 GLU Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 135 ARG Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 390 LEU Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 646 SER Chi-restraints excluded: chain 3 residue 657 LEU Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 282 GLU Chi-restraints excluded: chain 4 residue 410 MET Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 79 SER Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 185 ILE Chi-restraints excluded: chain d residue 320 ARG Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 69 GLU Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain g residue 25 ASN Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 257 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 166 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 329 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 461 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN e 47 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 12 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.073411 restraints weight = 23849.303| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.06 r_work: 0.2797 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 28790 Z= 0.417 Angle : 2.662 50.658 39003 Z= 1.533 Chirality : 0.483 6.552 4216 Planarity : 0.004 0.042 4995 Dihedral : 9.020 158.997 4201 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.04 % Allowed : 11.08 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3430 helix: 0.96 (0.14), residues: 1338 sheet: -0.64 (0.25), residues: 358 loop : 0.13 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 249 TYR 0.020 0.002 TYR 9 118 PHE 0.017 0.001 PHE i 55 TRP 0.011 0.001 TRP i 61 HIS 0.006 0.001 HIS 5 160 Details of bonding type rmsd/Z covalent geometry : bond 0.01211 / 0.42 (28754) covalent geometry : angle 2.32153 / 1.53 (38919) hydrogen bonds : bond 0.03774 / 2.48 ( 1122) hydrogen bonds : angle 5.00705 / 3.47 ( 3108) metal coordination : bond 0.03652 / 2.14 ( 36) metal coordination : angle 28.17084 / 17.55 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 429 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 431 GLN cc_start: 0.8486 (pp30) cc_final: 0.8190 (pp30) REVERT: 2 122 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8695 (tmmt) REVERT: 2 180 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8310 (mttp) REVERT: 3 246 GLU cc_start: 0.8542 (tt0) cc_final: 0.8316 (tt0) REVERT: 3 640 ASN cc_start: 0.8695 (t0) cc_final: 0.8372 (t0) REVERT: 6 81 ARG cc_start: 0.8638 (mtp180) cc_final: 0.7732 (tpt90) REVERT: 6 102 LYS cc_start: 0.9259 (tttt) cc_final: 0.9051 (tttm) REVERT: 6 174 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8281 (mpt-90) REVERT: 9 78 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9306 (pp) REVERT: c 28 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: d 52 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: d 320 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7979 (ttm170) REVERT: e 30 GLN cc_start: 0.9103 (tp40) cc_final: 0.8865 (tp-100) REVERT: f 29 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8787 (mtpt) REVERT: f 39 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8477 (mppt) REVERT: g 26 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8069 (pt0) REVERT: g 98 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8178 (mp-120) REVERT: h 17 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7699 (mmt-90) REVERT: h 47 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7966 (mtm-85) REVERT: i 8 LYS cc_start: 0.8787 (mttt) cc_final: 0.8301 (mptt) REVERT: i 21 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7471 (mpt180) REVERT: i 50 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8110 (tt0) REVERT: q 21 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8228 (mmtm) REVERT: q 26 ARG cc_start: 0.7872 (tmm160) cc_final: 0.7392 (tmm160) outliers start: 61 outliers final: 24 residues processed: 458 average time/residue: 0.8295 time to fit residues: 432.3094 Evaluate side-chains 449 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 416 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 324 GLN Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 122 LYS Chi-restraints excluded: chain 3 residue 135 ARG Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 390 LEU Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 646 SER Chi-restraints excluded: chain 3 residue 657 LEU Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 282 GLU Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 320 ARG Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 69 GLU Chi-restraints excluded: chain g residue 25 ASN Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain i residue 21 ARG Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain q residue 21 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 320 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 314 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 235 optimal weight: 30.0000 chunk 291 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 321 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 27 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 461 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 36 ASN d 184 ASN e 47 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN i 91 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.092542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071737 restraints weight = 23509.991| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.05 r_work: 0.2761 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9301 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.242 28790 Z= 0.441 Angle : 2.668 50.697 39003 Z= 1.536 Chirality : 0.487 6.677 4216 Planarity : 0.005 0.062 4995 Dihedral : 9.175 159.009 4201 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.87 % Allowed : 11.38 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3430 helix: 0.89 (0.14), residues: 1344 sheet: -0.49 (0.25), residues: 353 loop : 0.13 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 9 8 TYR 0.021 0.002 TYR 9 118 PHE 0.020 0.002 PHE i 55 TRP 0.012 0.001 TRP c 124 HIS 0.008 0.001 HIS 5 160 Details of bonding type rmsd/Z covalent geometry : bond 0.01251 / 0.44 (28754) covalent geometry : angle 2.33168 / 1.53 (38919) hydrogen bonds : bond 0.04178 / 2.75 ( 1122) hydrogen bonds : angle 5.10533 / 3.54 ( 3108) metal coordination : bond 0.04615 / 2.66 ( 36) metal coordination : angle 28.04739 / 17.48 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 423 time to evaluate : 1.329 Fit side-chains REVERT: 1 431 GLN cc_start: 0.8493 (pp30) cc_final: 0.8213 (pp30) REVERT: 2 180 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8314 (mttp) REVERT: 3 640 ASN cc_start: 0.8717 (t0) cc_final: 0.8427 (t0) REVERT: 6 81 ARG cc_start: 0.8630 (mtp180) cc_final: 0.7737 (tpt90) REVERT: 6 102 LYS cc_start: 0.9272 (tttt) cc_final: 0.9061 (tttm) REVERT: 6 174 ARG cc_start: 0.8670 (mtm-85) cc_final: 0.8295 (mpt-90) REVERT: a 47 SER cc_start: 0.8959 (p) cc_final: 0.8712 (p) REVERT: c 28 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: d 52 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: d 107 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: d 320 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7992 (ttm170) REVERT: e 30 GLN cc_start: 0.9128 (tp40) cc_final: 0.8880 (tp-100) REVERT: e 34 ASP cc_start: 0.8975 (m-30) cc_final: 0.8754 (m-30) REVERT: f 29 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8780 (mtpt) REVERT: f 39 LYS cc_start: 0.8726 (mtmm) cc_final: 0.8466 (mppt) REVERT: g 26 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: g 98 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: h 17 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7703 (mmt-90) REVERT: i 8 LYS cc_start: 0.8804 (mttt) cc_final: 0.8321 (mptt) REVERT: i 21 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7487 (mpt180) REVERT: i 50 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8107 (tt0) REVERT: q 21 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8261 (mmtm) REVERT: q 26 ARG cc_start: 0.7881 (tmm160) cc_final: 0.7398 (tmm160) outliers start: 56 outliers final: 30 residues processed: 452 average time/residue: 0.8617 time to fit residues: 443.7626 Evaluate side-chains 455 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 416 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 248 GLU Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 3 residue 135 ARG Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 390 LEU Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 646 SER Chi-restraints excluded: chain 3 residue 657 LEU Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 282 GLU Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 107 GLU Chi-restraints excluded: chain d residue 320 ARG Chi-restraints excluded: chain e residue 91 GLU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 69 GLU Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain g residue 25 ASN Chi-restraints excluded: chain g residue 26 GLU Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain i residue 21 ARG Chi-restraints excluded: chain j residue 20 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain q residue 21 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 254 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 356 HIS ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 461 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN d 203 GLN e 47 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.092693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.071924 restraints weight = 23536.306| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.05 r_work: 0.2766 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9300 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.239 28790 Z= 0.436 Angle : 2.668 50.666 39003 Z= 1.536 Chirality : 0.486 6.610 4216 Planarity : 0.005 0.052 4995 Dihedral : 9.179 159.064 4201 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.67 % Allowed : 11.92 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3430 helix: 0.89 (0.14), residues: 1345 sheet: -0.49 (0.25), residues: 353 loop : 0.16 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 1 249 TYR 0.021 0.002 TYR 9 118 PHE 0.019 0.002 PHE i 55 TRP 0.011 0.001 TRP 5 203 HIS 0.008 0.001 HIS 5 160 Details of bonding type rmsd/Z covalent geometry : bond 0.01242 / 0.43 (28754) covalent geometry : angle 2.33037 / 1.53 (38919) hydrogen bonds : bond 0.04102 / 2.70 ( 1122) hydrogen bonds : angle 5.09424 / 3.54 ( 3108) metal coordination : bond 0.04346 / 2.50 ( 36) metal coordination : angle 28.07205 / 17.49 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 416 time to evaluate : 1.153 Fit side-chains REVERT: 1 339 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8080 (mtp-110) REVERT: 1 431 GLN cc_start: 0.8495 (pp30) cc_final: 0.8204 (pp30) REVERT: 2 168 ASP cc_start: 0.8671 (m-30) cc_final: 0.8255 (m-30) REVERT: 2 180 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8311 (mttp) REVERT: 3 640 ASN cc_start: 0.8716 (t0) cc_final: 0.8408 (t0) REVERT: 4 63 ARG cc_start: 0.8917 (ttt180) cc_final: 0.8716 (ttt180) REVERT: 6 81 ARG cc_start: 0.8653 (mtp180) cc_final: 0.7754 (tpt90) REVERT: 6 102 LYS cc_start: 0.9274 (tttt) cc_final: 0.9062 (tttm) REVERT: 6 174 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8287 (mpt-90) REVERT: a 47 SER cc_start: 0.8959 (p) cc_final: 0.8715 (p) REVERT: c 28 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: d 52 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: d 107 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: d 320 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: e 30 GLN cc_start: 0.9130 (tp40) cc_final: 0.8917 (tp-100) REVERT: f 29 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8791 (mtpt) REVERT: f 39 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8458 (mppt) REVERT: g 26 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: g 98 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: h 17 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7690 (mmt-90) REVERT: i 8 LYS cc_start: 0.8801 (mttt) cc_final: 0.8299 (mptt) REVERT: i 21 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7506 (mpt180) REVERT: i 50 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8124 (tt0) REVERT: q 21 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8276 (mmtm) REVERT: q 26 ARG cc_start: 0.7889 (tmm160) cc_final: 0.7427 (tmm160) outliers start: 50 outliers final: 30 residues processed: 442 average time/residue: 0.8035 time to fit residues: 405.8696 Evaluate side-chains 453 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 414 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 135 ARG Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 390 LEU Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 646 SER Chi-restraints excluded: chain 3 residue 657 LEU Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 282 GLU Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 59 SER Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 107 GLU Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 320 ARG Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 69 GLU Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain g residue 25 ASN Chi-restraints excluded: chain g residue 26 GLU Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain i residue 21 ARG Chi-restraints excluded: chain j residue 20 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain q residue 21 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 132 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 16 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 461 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN d 203 GLN e 47 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.073581 restraints weight = 23572.410| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.05 r_work: 0.2800 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9275 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 28790 Z= 0.416 Angle : 2.666 51.136 39003 Z= 1.534 Chirality : 0.483 6.522 4216 Planarity : 0.004 0.040 4995 Dihedral : 8.999 159.243 4201 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.50 % Allowed : 12.12 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3430 helix: 0.97 (0.14), residues: 1338 sheet: -0.63 (0.26), residues: 358 loop : 0.23 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 5 14 TYR 0.020 0.002 TYR 9 118 PHE 0.017 0.001 PHE i 55 TRP 0.012 0.001 TRP i 61 HIS 0.006 0.001 HIS 5 160 Details of bonding type rmsd/Z covalent geometry : bond 0.01210 / 0.41 (28754) covalent geometry : angle 2.32417 / 1.53 (38919) hydrogen bonds : bond 0.03733 / 2.46 ( 1122) hydrogen bonds : angle 4.99693 / 3.47 ( 3108) metal coordination : bond 0.03573 / 2.06 ( 36) metal coordination : angle 28.23277 / 17.57 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 412 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: 1 339 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8030 (mtp-110) REVERT: 1 431 GLN cc_start: 0.8488 (pp30) cc_final: 0.8198 (pp30) REVERT: 2 180 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8312 (mttp) REVERT: 3 640 ASN cc_start: 0.8705 (t0) cc_final: 0.8399 (t0) REVERT: 6 81 ARG cc_start: 0.8634 (mtp180) cc_final: 0.7741 (tpt90) REVERT: 6 102 LYS cc_start: 0.9250 (tttt) cc_final: 0.9040 (tttm) REVERT: 6 174 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8275 (mpt-90) REVERT: 9 78 ILE cc_start: 0.9595 (OUTLIER) cc_final: 0.9265 (pp) REVERT: c 28 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: d 52 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: d 107 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: d 320 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8009 (ttm170) REVERT: e 30 GLN cc_start: 0.9110 (tp40) cc_final: 0.8790 (tp-100) REVERT: e 39 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8422 (mtt90) REVERT: f 29 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8774 (mtpt) REVERT: f 39 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8445 (mppt) REVERT: g 26 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8052 (pt0) REVERT: g 98 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8124 (mp10) REVERT: h 17 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7669 (mmt-90) REVERT: h 111 TYR cc_start: 0.7779 (m-10) cc_final: 0.7552 (m-10) REVERT: i 8 LYS cc_start: 0.8793 (mttt) cc_final: 0.8295 (mptt) REVERT: i 21 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7499 (mpt180) REVERT: i 50 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8128 (tt0) REVERT: q 26 ARG cc_start: 0.7873 (tmm160) cc_final: 0.7455 (tmm160) outliers start: 45 outliers final: 28 residues processed: 440 average time/residue: 0.8057 time to fit residues: 404.8214 Evaluate side-chains 443 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 407 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 93 LYS Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 135 ARG Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 390 LEU Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 646 SER Chi-restraints excluded: chain 3 residue 657 LEU Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 189 MET Chi-restraints excluded: chain 4 residue 282 GLU Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 37 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 107 GLU Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 320 ARG Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 69 GLU Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain i residue 21 ARG Chi-restraints excluded: chain j residue 20 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 65 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 333 optimal weight: 9.9990 chunk 334 optimal weight: 0.0980 chunk 303 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 16 GLN 3 119 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 461 ASN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN 6 162 GLN a 35 ASN d 184 ASN d 203 GLN e 47 ASN e 92 ASN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.077500 restraints weight = 24331.542| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.07 r_work: 0.2879 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 28790 Z= 0.406 Angle : 2.669 57.306 39003 Z= 1.532 Chirality : 0.479 6.442 4216 Planarity : 0.004 0.038 4995 Dihedral : 8.628 158.799 4201 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.07 % Allowed : 12.58 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3430 helix: 1.09 (0.14), residues: 1328 sheet: -0.61 (0.26), residues: 355 loop : 0.24 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 1 249 TYR 0.020 0.001 TYR 4 275 PHE 0.014 0.001 PHE 4 349 TRP 0.015 0.001 TRP i 61 HIS 0.006 0.001 HIS i 87 Details of bonding type rmsd/Z covalent geometry : bond 0.01198 / 0.41 (28754) covalent geometry : angle 2.31765 / 1.53 (38919) hydrogen bonds : bond 0.03202 / 2.10 ( 1122) hydrogen bonds : angle 4.79070 / 3.32 ( 3108) metal coordination : bond 0.02483 / 1.43 ( 36) metal coordination : angle 28.60050 / 17.77 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13959.42 seconds wall clock time: 237 minutes 36.10 seconds (14256.10 seconds total)