Starting phenix.real_space_refine on Tue May 5 22:12:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnw_38517/05_2026/8xnw_38517_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnw_38517/05_2026/8xnw_38517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnw_38517/05_2026/8xnw_38517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnw_38517/05_2026/8xnw_38517.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnw_38517/05_2026/8xnw_38517_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnw_38517/05_2026/8xnw_38517_neut.cif" } resolution = 3.6 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= 0.001 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 9 5.49 5 S 246 5.16 5 C 21663 2.51 5 N 5755 2.21 5 O 6146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33848 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain: "C" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1636 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Chain: "D" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3088 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 21, 'TRANS': 363} Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3288 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2532 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 22, 'TRANS': 294} Chain breaks: 1 Chain: "I" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1380 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain breaks: 1 Chain: "P" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2720 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 940 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1145 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "q" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 951 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain breaks: 2 Chain: "r" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 354 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 6, 'TRANS': 37} Chain breaks: 2 Chain: "s" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 193 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PC1': 1, 'SF4': 1, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-3': 1, 'UQ9:plan-4': 1, 'UQ9:plan-5': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'UQ9': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1178 SG CYS B 99 80.773 63.378 105.627 1.00 29.52 S ATOM 1681 SG CYS B 164 78.050 59.601 110.426 1.00 28.96 S ATOM 1911 SG CYS B 194 83.219 59.707 109.786 1.00 29.28 S ATOM 1184 SG CYS B 100 79.664 59.394 104.644 1.00 30.11 S ATOM 7686 SG CYS E 134 139.631 55.437 153.329 1.00 56.01 S ATOM 7720 SG CYS E 139 142.382 57.351 152.522 1.00 56.50 S ATOM 8004 SG CYS E 175 137.171 58.873 155.921 1.00 54.42 S ATOM 8027 SG CYS E 179 140.324 60.903 155.785 1.00 57.95 S ATOM 11557 SG CYS F 425 120.637 63.891 155.917 1.00 45.60 S ATOM 11235 SG CYS F 385 120.903 61.633 150.042 1.00 39.95 S ATOM 11215 SG CYS F 382 116.542 62.536 152.248 1.00 40.29 S ATOM 11196 SG CYS F 379 118.608 58.452 155.010 1.00 43.09 S ATOM 12605 SG CYS G 131 101.225 51.191 137.897 1.00 31.31 S ATOM 12584 SG CYS G 128 103.182 55.271 133.487 1.00 30.26 S ATOM 12645 SG CYS G 137 100.611 57.023 139.515 1.00 33.13 S ATOM 13330 SG CYS G 226 102.552 50.958 146.519 1.00 34.31 S ATOM 13001 SG CYS G 182 105.547 49.504 151.771 1.00 36.31 S ATOM 12977 SG CYS G 179 104.835 54.845 149.924 1.00 35.62 S ATOM 12954 SG CYS G 176 108.510 50.814 147.397 1.00 34.05 S ATOM 12091 SG CYS G 64 105.940 60.863 152.180 1.00 35.53 S ATOM 12177 SG CYS G 75 106.621 62.991 150.605 1.00 36.47 S ATOM 12202 SG CYS G 78 105.254 67.427 152.874 1.00 36.76 S ATOM 12303 SG CYS G 92 102.838 65.190 154.681 1.00 39.04 S ATOM 20533 SG CYS I 152 87.294 53.354 113.619 1.00 27.39 S ATOM 20307 SG CYS I 123 86.768 54.304 119.000 1.00 27.30 S ATOM 20559 SG CYS I 155 89.516 58.212 115.415 1.00 27.04 S ATOM 20580 SG CYS I 158 92.787 53.078 116.222 1.00 26.60 S ATOM 20279 SG CYS I 119 92.987 50.212 122.618 1.00 28.85 S ATOM 20609 SG CYS I 162 99.297 50.240 120.631 1.00 28.07 S ATOM 20237 SG CYS I 113 95.981 45.178 122.750 1.00 28.61 S ATOM 20256 SG CYS I 116 98.218 49.517 126.573 1.00 29.24 S ATOM 25091 SG CYS R 79 112.531 43.832 125.669 1.00 32.60 S ATOM 25267 SG CYS R 104 110.106 42.332 127.020 1.00 32.49 S ATOM 25289 SG CYS R 107 109.496 43.080 123.603 1.00 30.78 S Time building chain proxies: 7.69, per 1000 atoms: 0.23 Number of scatterers: 33848 At special positions: 0 Unit cell: (167.2, 130.9, 203.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 246 16.00 P 9 15.00 O 6146 8.00 N 5755 7.00 C 21663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS X 36 " - pdb=" SG CYS X 66 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.04 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.03 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE1 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 116 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7842 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 35 sheets defined 49.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.314A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'B' and resid 70 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.583A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 4.249A pdb=" N PHE B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 118 " --> pdb=" O MET B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 118' Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 4.067A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.320A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 159 through 160 No H-bonds generated for 'chain 'C' and resid 159 through 160' Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.034A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.588A pdb=" N HIS D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.967A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.455A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.772A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.843A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.707A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 3.691A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.668A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.530A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.620A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.608A pdb=" N ASN E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.612A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.557A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.296A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 removed outlier: 4.184A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 4.032A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.636A pdb=" N GLY F 188 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 4.261A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 257 removed outlier: 3.587A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing helix chain 'F' and resid 258 through 266 removed outlier: 4.015A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.860A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.733A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.547A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.662A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.722A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.348A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.519A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.599A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.774A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.712A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 200 through 204 Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.821A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 361 Processing helix chain 'G' and resid 377 through 386 removed outlier: 4.302A pdb=" N LEU G 381 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG G 382 " --> pdb=" O THR G 379 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER G 383 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.588A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.025A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.009A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.677A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 529 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 556 through 560 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 665 through 675 Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.642A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.750A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.575A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 85 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 100 through 124 removed outlier: 3.687A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.853A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.735A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 242 removed outlier: 4.207A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU H 227 " --> pdb=" O PHE H 223 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR H 228 " --> pdb=" O PHE H 224 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 235 " --> pdb=" O ILE H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 277 Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 61 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.910A pdb=" N ILE I 67 " --> pdb=" O TRP I 63 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 187 through 195 removed outlier: 3.584A pdb=" N ASN I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN I 193 " --> pdb=" O LYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 209 removed outlier: 4.285A pdb=" N ALA I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN I 204 " --> pdb=" O GLU I 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 76 Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.589A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 91 through 96' Processing helix chain 'P' and resid 114 through 122 removed outlier: 4.504A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 Processing helix chain 'P' and resid 178 through 195 Processing helix chain 'P' and resid 213 through 220 Processing helix chain 'P' and resid 228 through 233 removed outlier: 3.773A pdb=" N LEU P 231 " --> pdb=" O LEU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 255 through 259 Processing helix chain 'P' and resid 273 through 284 removed outlier: 4.118A pdb=" N GLY P 282 " --> pdb=" O LYS P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.936A pdb=" N LEU P 304 " --> pdb=" O TRP P 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE P 305 " --> pdb=" O ILE P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 Processing helix chain 'P' and resid 334 through 339 Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.445A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 72 Processing helix chain 'Q' and resid 130 through 142 removed outlier: 3.520A pdb=" N PHE Q 137 " --> pdb=" O ASP Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 165 Processing helix chain 'R' and resid 42 through 49 removed outlier: 4.168A pdb=" N ARG R 47 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'S' and resid 32 through 48 removed outlier: 6.311A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS S 46 " --> pdb=" O VAL S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 Processing helix chain 'T' and resid 111 through 127 removed outlier: 3.591A pdb=" N VAL T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU T 117 " --> pdb=" O LEU T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 138 Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 35 Processing helix chain 'V' and resid 36 through 38 No H-bonds generated for 'chain 'V' and resid 36 through 38' Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.709A pdb=" N GLN V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU V 54 " --> pdb=" O GLN V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 73 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.681A pdb=" N LYS V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.991A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 Processing helix chain 'W' and resid 78 through 98 removed outlier: 3.947A pdb=" N ILE W 87 " --> pdb=" O ASP W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 108 Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'X' and resid 9 through 14 Processing helix chain 'X' and resid 21 through 28 removed outlier: 3.544A pdb=" N LEU X 25 " --> pdb=" O SER X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 35 Processing helix chain 'X' and resid 37 through 50 removed outlier: 3.680A pdb=" N GLU X 42 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE X 43 " --> pdb=" O THR X 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU X 49 " --> pdb=" O LEU X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 77 removed outlier: 4.056A pdb=" N LEU X 68 " --> pdb=" O ASN X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.893A pdb=" N CYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 removed outlier: 3.900A pdb=" N ALA X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS X 110 " --> pdb=" O LYS X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 144 Processing helix chain 'Z' and resid 31 through 87 removed outlier: 3.544A pdb=" N GLY Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG Z 68 " --> pdb=" O ASP Z 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Proline residue: Z 73 - end of helix removed outlier: 3.659A pdb=" N LEU Z 87 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 96 removed outlier: 3.717A pdb=" N GLU Z 93 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 138 Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 17 through 27 Processing helix chain 'a' and resid 41 through 55 removed outlier: 3.740A pdb=" N TRP a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 4.032A pdb=" N ASN b 11 " --> pdb=" O ALA b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 23 Processing helix chain 'b' and resid 24 through 35 removed outlier: 3.580A pdb=" N ALA b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE b 30 " --> pdb=" O TRP b 26 " (cutoff:3.500A) Proline residue: b 33 - end of helix Processing helix chain 'b' and resid 38 through 40 No H-bonds generated for 'chain 'b' and resid 38 through 40' Processing helix chain 'b' and resid 41 through 49 removed outlier: 3.534A pdb=" N ASN b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS b 47 " --> pdb=" O SER b 43 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.740A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS q 8 " --> pdb=" O VAL q 4 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 27 Processing helix chain 'q' and resid 43 through 45 No H-bonds generated for 'chain 'q' and resid 43 through 45' Processing helix chain 'q' and resid 78 through 82 removed outlier: 4.201A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 3.984A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 16 Processing helix chain 's' and resid 78 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 93 removed outlier: 4.541A pdb=" N ILE B 132 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.858A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C 83 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.400A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'D' and resid 82 through 84 removed outlier: 4.107A pdb=" N ARG D 96 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 100 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 108 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'D' and resid 397 through 401 removed outlier: 3.500A pdb=" N PHE D 407 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 168 through 171 removed outlier: 6.566A pdb=" N TYR E 129 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE E 171 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 131 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.151A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.598A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB4, first strand: chain 'G' and resid 35 through 36 removed outlier: 6.776A pdb=" N PHE G 35 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AB7, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.349A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 306 through 309 Processing sheet with id=AB9, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.096A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N CYS G 367 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA G 340 " --> pdb=" O CYS G 367 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.323A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASN G 514 " --> pdb=" O PRO G 472 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL G 474 " --> pdb=" O ASN G 514 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC3, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AC4, first strand: chain 'I' and resid 132 through 134 removed outlier: 3.573A pdb=" N ARG I 141 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 146 through 148 Processing sheet with id=AC6, first strand: chain 'P' and resid 56 through 58 removed outlier: 5.863A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE P 201 " --> pdb=" O PHE P 164 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N HIS P 166 " --> pdb=" O ILE P 201 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE P 200 " --> pdb=" O PHE P 263 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE P 265 " --> pdb=" O ILE P 200 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG P 202 " --> pdb=" O PHE P 265 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 80 through 84 removed outlier: 3.849A pdb=" N LEU P 106 " --> pdb=" O ILE P 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 205 through 207 removed outlier: 6.369A pdb=" N ASP P 205 " --> pdb=" O VAL P 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'P' and resid 236 through 237 Processing sheet with id=AD1, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AD2, first strand: chain 'Q' and resid 78 through 80 removed outlier: 4.055A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU Q 126 " --> pdb=" O MET Q 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD5, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.507A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 55 through 57 Processing sheet with id=AD7, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD8, first strand: chain 'q' and resid 38 through 41 1355 hydrogen bonds defined for protein. 3849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.35 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 11464 1.37 - 1.58: 22739 1.58 - 1.80: 218 1.80 - 2.01: 167 2.01 - 2.23: 80 Bond restraints: 34668 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.647 0.731 2.00e-02 2.50e+03 1.34e+03 bond pdb=" CA7 CDL q 201 " pdb=" OA8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CB7 CDL q 201 " pdb=" OB8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.449 -0.115 1.10e-02 8.26e+03 1.10e+02 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.399 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C ARG Q 106 " pdb=" O ARG Q 106 " ideal model delta sigma weight residual 1.236 1.339 -0.103 1.14e-02 7.69e+03 8.14e+01 ... (remaining 34663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.45: 46270 6.45 - 12.90: 567 12.90 - 19.35: 165 19.35 - 25.80: 3 25.80 - 32.25: 2 Bond angle restraints: 47007 Sorted by residual: angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.00 25.64 1.52e+00 4.33e-01 2.85e+02 angle pdb=" N CYS F 125 " pdb=" CA CYS F 125 " pdb=" C CYS F 125 " ideal model delta sigma weight residual 113.17 93.47 19.70 1.26e+00 6.30e-01 2.44e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.80 16.53 1.14e+00 7.69e-01 2.10e+02 angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.59 16.74 1.20e+00 6.94e-01 1.95e+02 angle pdb=" N MET G 77 " pdb=" CA MET G 77 " pdb=" C MET G 77 " ideal model delta sigma weight residual 113.38 97.32 16.06 1.23e+00 6.61e-01 1.70e+02 ... (remaining 47002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 20548 35.19 - 70.38: 308 70.38 - 105.57: 34 105.57 - 140.77: 2 140.77 - 175.96: 1 Dihedral angle restraints: 20893 sinusoidal: 8730 harmonic: 12163 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 171.69 -78.69 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" CB CYS X 78 " pdb=" SG CYS X 78 " pdb=" SG CYS X 110 " pdb=" CB CYS X 110 " ideal model delta sinusoidal sigma weight residual 93.00 154.31 -61.31 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" N THR Z 144 " pdb=" C THR Z 144 " pdb=" CA THR Z 144 " pdb=" CB THR Z 144 " ideal model delta harmonic sigma weight residual 123.40 107.48 15.92 0 2.50e+00 1.60e-01 4.06e+01 ... (remaining 20890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 4710 0.191 - 0.382: 391 0.382 - 0.573: 22 0.573 - 0.764: 3 0.764 - 0.955: 24 Chirality restraints: 5150 Sorted by residual: chirality pdb="FE3 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.60 -0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb="FE1 SF4 I 303 " pdb=" S2 SF4 I 303 " pdb=" S3 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.92 2.00e-01 2.50e+01 2.11e+01 chirality pdb="FE2 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S3 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False 10.55 9.64 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 5147 not shown) Planarity restraints: 5975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 400 " 0.013 2.00e-02 2.50e+03 2.72e-01 2.22e+03 pdb=" C1M UQ9 H 400 " 0.133 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 400 " -0.157 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 400 " 0.128 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 400 " 0.012 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 400 " -0.117 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 400 " 0.069 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 400 " 0.345 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 400 " -0.542 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 400 " 0.498 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 400 " 0.005 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 400 " -0.386 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 B 302 " -0.058 2.00e-02 2.50e+03 2.23e-01 1.49e+03 pdb=" C1M UQ9 B 302 " -0.209 2.00e-02 2.50e+03 pdb=" C2 UQ9 B 302 " -0.050 2.00e-02 2.50e+03 pdb=" C3 UQ9 B 302 " 0.109 2.00e-02 2.50e+03 pdb=" C4 UQ9 B 302 " -0.017 2.00e-02 2.50e+03 pdb=" C5 UQ9 B 302 " -0.107 2.00e-02 2.50e+03 pdb=" C6 UQ9 B 302 " 0.086 2.00e-02 2.50e+03 pdb=" C7 UQ9 B 302 " 0.499 2.00e-02 2.50e+03 pdb=" O2 UQ9 B 302 " -0.190 2.00e-02 2.50e+03 pdb=" O3 UQ9 B 302 " 0.338 2.00e-02 2.50e+03 pdb=" O4 UQ9 B 302 " -0.068 2.00e-02 2.50e+03 pdb=" O5 UQ9 B 302 " -0.333 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 H 400 " -0.015 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C11 UQ9 H 400 " 0.104 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 400 " 0.133 2.00e-02 2.50e+03 pdb=" C8 UQ9 H 400 " -0.176 2.00e-02 2.50e+03 pdb=" C9 UQ9 H 400 " -0.046 2.00e-02 2.50e+03 ... (remaining 5972 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 445 2.53 - 3.13: 31061 3.13 - 3.72: 54064 3.72 - 4.31: 81647 4.31 - 4.90: 128518 Nonbonded interactions: 295735 Sorted by model distance: nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.942 3.040 nonbonded pdb=" O ASN H 97 " pdb=" OD1 ASN H 97 " model vdw 1.983 3.040 nonbonded pdb=" OD1 ASP C 147 " pdb=" OE1 GLU C 148 " model vdw 2.000 3.040 nonbonded pdb=" O PHE G 63 " pdb=" SG CYS G 64 " model vdw 2.007 3.400 nonbonded pdb=" O ASN Z 24 " pdb=" OD1 ASN Z 24 " model vdw 2.045 3.040 ... (remaining 295730 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 group one per residue 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.390 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 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 : 0.021 1.241 34709 Z= 1.009 Angle : 2.162 43.608 47099 Z= 1.432 Chirality : 0.122 0.955 5150 Planarity : 0.009 0.272 5975 Dihedral : 12.754 175.958 13039 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 47.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.47 % Favored : 92.46 % Rotamer: Outliers : 0.44 % Allowed : 7.51 % Favored : 92.05 % Cbeta Deviations : 1.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.12), residues: 4136 helix: -1.79 (0.11), residues: 1773 sheet: -2.17 (0.27), residues: 327 loop : -2.40 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 68 TYR 0.046 0.003 TYR B 112 PHE 0.031 0.002 PHE I 175 TRP 0.033 0.002 TRP G 285 HIS 0.018 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.01455 (34668) covalent geometry : angle 2.05415 (47007) SS BOND : bond 0.00917 ( 4) SS BOND : angle 1.31875 ( 8) hydrogen bonds : bond 0.24974 ( 1355) hydrogen bonds : angle 9.63595 ( 3849) metal coordination : bond 0.47155 ( 37) metal coordination : angle 16.08247 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1725 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 1709 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.7180 (tpp80) cc_final: 0.6855 (ptt180) REVERT: B 88 SER cc_start: 0.7950 (p) cc_final: 0.7691 (p) REVERT: B 196 PRO cc_start: 0.7629 (Cg_exo) cc_final: 0.7344 (Cg_endo) REVERT: B 201 LEU cc_start: 0.9231 (tp) cc_final: 0.8516 (tp) REVERT: C 133 SER cc_start: 0.7504 (t) cc_final: 0.7292 (p) REVERT: C 178 PHE cc_start: 0.7004 (m-10) cc_final: 0.6598 (m-10) REVERT: D 144 MET cc_start: 0.7311 (mpp) cc_final: 0.6880 (mpp) REVERT: F 349 LEU cc_start: 0.6150 (tp) cc_final: 0.4818 (tp) REVERT: F 361 THR cc_start: 0.7066 (p) cc_final: 0.6262 (p) REVERT: G 144 MET cc_start: 0.8021 (tpt) cc_final: 0.7680 (tpt) REVERT: G 496 MET cc_start: 0.6363 (ttp) cc_final: 0.6130 (ttp) REVERT: H 277 TYR cc_start: 0.6865 (m-10) cc_final: 0.6540 (m-80) REVERT: H 285 LEU cc_start: 0.8568 (tt) cc_final: 0.8303 (tp) REVERT: P 328 MET cc_start: 0.7951 (tpt) cc_final: 0.7731 (tpt) REVERT: Q 160 TYR cc_start: 0.8117 (t80) cc_final: 0.7902 (t80) REVERT: Q 164 PHE cc_start: 0.5859 (m-80) cc_final: 0.5149 (m-80) REVERT: T 86 VAL cc_start: 0.7520 (t) cc_final: 0.7235 (t) REVERT: T 103 HIS cc_start: 0.6689 (m-70) cc_final: 0.6476 (m90) REVERT: T 105 MET cc_start: 0.7606 (mmt) cc_final: 0.7170 (mmt) REVERT: W 61 GLN cc_start: 0.6612 (tt0) cc_final: 0.6342 (tt0) REVERT: W 118 PRO cc_start: 0.8112 (Cg_exo) cc_final: 0.7908 (Cg_endo) REVERT: X 47 ARG cc_start: 0.6786 (tpt170) cc_final: 0.6406 (tmt170) REVERT: X 69 ASN cc_start: 0.7552 (t0) cc_final: 0.7098 (t0) REVERT: b 11 ASN cc_start: 0.5713 (p0) cc_final: 0.5422 (p0) REVERT: q 89 TRP cc_start: 0.7249 (t60) cc_final: 0.6921 (t60) outliers start: 16 outliers final: 1 residues processed: 1713 average time/residue: 0.2326 time to fit residues: 625.6511 Evaluate side-chains 1008 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1007 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 166 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 102 HIS C 104 ASN C 195 HIS D 117 HIS D 131 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN D 346 GLN D 381 HIS E 68 ASN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS E 181 ASN E 190 ASN E 245 GLN F 220 GLN F 344 GLN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN F 451 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 ASN G 331 GLN G 388 ASN ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 495 ASN ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 604 GLN G 605 GLN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS P 71 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN P 251 ASN P 341 GLN Q 71 HIS ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN S 92 GLN V 41 HIS W 61 GLN W 105 HIS Z 8 GLN Z 54 ASN Z 76 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 ASN b 71 GLN r 13 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.100753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083198 restraints weight = 103268.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.085985 restraints weight = 47380.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.087811 restraints weight = 27895.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.088989 restraints weight = 19367.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089771 restraints weight = 15200.249| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 34709 Z= 0.211 Angle : 1.080 69.614 47099 Z= 0.452 Chirality : 0.049 0.310 5150 Planarity : 0.007 0.124 5975 Dihedral : 9.168 132.948 4796 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 3.88 % Allowed : 18.23 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.12), residues: 4136 helix: -0.51 (0.11), residues: 1835 sheet: -1.88 (0.26), residues: 343 loop : -1.85 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 34 TYR 0.043 0.003 TYR B 170 PHE 0.035 0.003 PHE H 19 TRP 0.027 0.002 TRP A 106 HIS 0.016 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00478 (34668) covalent geometry : angle 0.86889 (47007) SS BOND : bond 0.00252 ( 4) SS BOND : angle 1.32985 ( 8) hydrogen bonds : bond 0.06189 ( 1355) hydrogen bonds : angle 6.06120 ( 3849) metal coordination : bond 0.02094 ( 37) metal coordination : angle 15.20179 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1152 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7751 (mtm) cc_final: 0.7056 (mtm) REVERT: A 48 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7076 (ptt180) REVERT: B 79 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.7953 (t0) REVERT: B 80 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8281 (t0) REVERT: B 83 ASN cc_start: 0.8482 (m110) cc_final: 0.7285 (m-40) REVERT: B 126 ARG cc_start: 0.8913 (tpp-160) cc_final: 0.8519 (tpp-160) REVERT: B 151 GLN cc_start: 0.8989 (mt0) cc_final: 0.8503 (mt0) REVERT: B 211 LYS cc_start: 0.8513 (tttt) cc_final: 0.8307 (ttmt) REVERT: C 106 GLN cc_start: 0.8206 (mp10) cc_final: 0.7828 (mp10) REVERT: C 133 SER cc_start: 0.8457 (t) cc_final: 0.7780 (p) REVERT: C 178 PHE cc_start: 0.7635 (m-10) cc_final: 0.7427 (m-10) REVERT: C 216 LYS cc_start: 0.9146 (mptt) cc_final: 0.8942 (mptt) REVERT: D 79 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6796 (t0) REVERT: D 101 LEU cc_start: 0.9116 (mt) cc_final: 0.8732 (mt) REVERT: D 105 MET cc_start: 0.8451 (mmm) cc_final: 0.8089 (tpp) REVERT: D 197 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7918 (ptp) REVERT: D 443 MET cc_start: 0.7220 (mmt) cc_final: 0.6170 (mmt) REVERT: E 83 ASP cc_start: 0.9136 (t0) cc_final: 0.8890 (t0) REVERT: E 112 TYR cc_start: 0.9100 (m-80) cc_final: 0.8705 (m-80) REVERT: E 184 MET cc_start: 0.7690 (ttp) cc_final: 0.7224 (ptp) REVERT: E 191 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: F 112 TYR cc_start: 0.8485 (m-80) cc_final: 0.7954 (m-80) REVERT: F 131 MET cc_start: 0.9127 (mmm) cc_final: 0.8093 (tmm) REVERT: F 157 TYR cc_start: 0.8376 (t80) cc_final: 0.7933 (t80) REVERT: F 206 CYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8290 (t) REVERT: F 262 PHE cc_start: 0.8553 (m-80) cc_final: 0.8045 (t80) REVERT: G 66 HIS cc_start: 0.8753 (t-90) cc_final: 0.8527 (t-90) REVERT: G 67 GLU cc_start: 0.8394 (tt0) cc_final: 0.7987 (tm-30) REVERT: G 471 LYS cc_start: 0.8887 (mttp) cc_final: 0.8672 (mtmm) REVERT: G 513 MET cc_start: 0.9061 (tpp) cc_final: 0.8806 (tpp) REVERT: G 548 LEU cc_start: 0.8562 (tp) cc_final: 0.8248 (tp) REVERT: H 59 GLU cc_start: 0.8072 (tt0) cc_final: 0.7784 (tt0) REVERT: H 68 MET cc_start: 0.6702 (pmm) cc_final: 0.6310 (ttp) REVERT: H 114 TYR cc_start: 0.7647 (m-80) cc_final: 0.7338 (m-80) REVERT: H 199 ASP cc_start: 0.7532 (t0) cc_final: 0.7151 (t0) REVERT: I 204 ASN cc_start: 0.8864 (m110) cc_final: 0.8502 (t0) REVERT: I 206 GLN cc_start: 0.8204 (tp40) cc_final: 0.7890 (tp40) REVERT: I 209 TYR cc_start: 0.9080 (p90) cc_final: 0.8813 (p90) REVERT: P 217 PHE cc_start: 0.8304 (m-80) cc_final: 0.8057 (m-80) REVERT: P 298 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8322 (t80) REVERT: P 319 VAL cc_start: 0.9480 (t) cc_final: 0.9278 (t) REVERT: P 350 ILE cc_start: 0.9248 (tp) cc_final: 0.9045 (tp) REVERT: P 351 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8121 (mm-30) REVERT: P 367 GLU cc_start: 0.7957 (mp0) cc_final: 0.7350 (pm20) REVERT: Q 58 LYS cc_start: 0.8972 (mtmm) cc_final: 0.8569 (mmtt) REVERT: Q 85 ASN cc_start: 0.8588 (t0) cc_final: 0.8187 (t0) REVERT: Q 100 GLU cc_start: 0.8100 (tp30) cc_final: 0.7883 (tp30) REVERT: Q 112 MET cc_start: 0.7814 (mmm) cc_final: 0.7544 (tpt) REVERT: Q 124 MET cc_start: 0.8780 (tpp) cc_final: 0.8238 (mmm) REVERT: R 74 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8896 (m-70) REVERT: S 44 LEU cc_start: 0.9336 (tp) cc_final: 0.9100 (tt) REVERT: T 103 HIS cc_start: 0.8223 (m-70) cc_final: 0.7998 (m90) REVERT: T 139 MET cc_start: 0.6753 (mtt) cc_final: 0.6372 (ttm) REVERT: T 143 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7672 (mt-10) REVERT: V 53 ASN cc_start: 0.9018 (m-40) cc_final: 0.8798 (m-40) REVERT: V 54 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8342 (pp20) REVERT: W 58 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7316 (m) REVERT: W 99 VAL cc_start: 0.8868 (t) cc_final: 0.8517 (t) REVERT: W 118 PRO cc_start: 0.8291 (Cg_exo) cc_final: 0.7947 (Cg_endo) REVERT: X 47 ARG cc_start: 0.8253 (tpt170) cc_final: 0.6697 (tmt170) REVERT: X 69 ASN cc_start: 0.9020 (t0) cc_final: 0.8590 (t0) REVERT: Z 80 ASP cc_start: 0.7962 (m-30) cc_final: 0.7484 (m-30) REVERT: Z 86 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8592 (tp) REVERT: Z 93 GLU cc_start: 0.8172 (tp30) cc_final: 0.7964 (tp30) REVERT: Z 114 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8135 (p) REVERT: a 5 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9216 (mm) REVERT: a 61 TYR cc_start: 0.7588 (t80) cc_final: 0.7320 (t80) REVERT: b 11 ASN cc_start: 0.8108 (p0) cc_final: 0.7741 (p0) REVERT: b 43 SER cc_start: 0.9013 (p) cc_final: 0.8676 (m) REVERT: b 47 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8411 (ttpp) REVERT: b 71 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8103 (mm110) outliers start: 141 outliers final: 62 residues processed: 1210 average time/residue: 0.2085 time to fit residues: 413.4787 Evaluate side-chains 996 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 921 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 206 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 462 PHE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 266 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 368 GLU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 71 GLN Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 68 optimal weight: 0.8980 chunk 353 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 384 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN C 74 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 303 HIS F 346 GLN ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN I 180 HIS P 71 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN W 94 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.097984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.080417 restraints weight = 103153.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.083106 restraints weight = 47512.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084889 restraints weight = 28308.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086115 restraints weight = 19819.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086876 restraints weight = 15407.797| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34709 Z= 0.184 Angle : 0.985 73.844 47099 Z= 0.391 Chirality : 0.046 0.232 5150 Planarity : 0.006 0.126 5975 Dihedral : 8.622 143.751 4792 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 4.21 % Allowed : 20.21 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 4136 helix: -0.01 (0.12), residues: 1841 sheet: -1.54 (0.27), residues: 344 loop : -1.58 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 86 TYR 0.034 0.002 TYR D 135 PHE 0.026 0.002 PHE A 62 TRP 0.028 0.002 TRP A 106 HIS 0.008 0.001 HIS b 69 Details of bonding type rmsd covalent geometry : bond 0.00422 (34668) covalent geometry : angle 0.76228 (47007) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.98636 ( 8) hydrogen bonds : bond 0.04870 ( 1355) hydrogen bonds : angle 5.50591 ( 3849) metal coordination : bond 0.02148 ( 37) metal coordination : angle 14.78248 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 997 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7701 (mtm) cc_final: 0.7238 (mtm) REVERT: A 35 ASN cc_start: 0.8562 (m-40) cc_final: 0.8335 (m-40) REVERT: A 38 GLU cc_start: 0.8251 (tt0) cc_final: 0.7862 (tt0) REVERT: A 48 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7080 (ptt180) REVERT: A 55 PHE cc_start: 0.9065 (p90) cc_final: 0.8173 (p90) REVERT: A 68 GLU cc_start: 0.8440 (tt0) cc_final: 0.8060 (tt0) REVERT: A 94 LEU cc_start: 0.9003 (tp) cc_final: 0.8699 (tp) REVERT: B 83 ASN cc_start: 0.8471 (m110) cc_final: 0.7870 (m110) REVERT: B 103 GLU cc_start: 0.8203 (tp30) cc_final: 0.7480 (tp30) REVERT: B 129 ASP cc_start: 0.8370 (m-30) cc_final: 0.7699 (m-30) REVERT: B 151 GLN cc_start: 0.8937 (mt0) cc_final: 0.8562 (mt0) REVERT: C 106 GLN cc_start: 0.8243 (mp10) cc_final: 0.7612 (mp10) REVERT: C 178 PHE cc_start: 0.7729 (m-10) cc_final: 0.7508 (m-10) REVERT: C 216 LYS cc_start: 0.9162 (mptt) cc_final: 0.8885 (mptt) REVERT: C 221 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7660 (mt-10) REVERT: D 79 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6972 (t0) REVERT: D 101 LEU cc_start: 0.9169 (mt) cc_final: 0.8816 (mt) REVERT: D 104 GLU cc_start: 0.7654 (tt0) cc_final: 0.7105 (tt0) REVERT: D 212 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 443 MET cc_start: 0.7209 (mmt) cc_final: 0.6280 (mmt) REVERT: E 45 GLU cc_start: 0.8685 (mp0) cc_final: 0.8447 (mp0) REVERT: E 83 ASP cc_start: 0.9189 (t0) cc_final: 0.8811 (t0) REVERT: E 122 ASN cc_start: 0.7224 (t0) cc_final: 0.6764 (t0) REVERT: E 184 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7104 (ptt) REVERT: E 191 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: F 75 TRP cc_start: 0.7544 (t60) cc_final: 0.7047 (t60) REVERT: F 337 MET cc_start: 0.8522 (tpp) cc_final: 0.7888 (tpp) REVERT: F 349 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.5282 (tp) REVERT: F 457 HIS cc_start: 0.5472 (m-70) cc_final: 0.4596 (p-80) REVERT: G 67 GLU cc_start: 0.8422 (tt0) cc_final: 0.7783 (tm-30) REVERT: G 117 MET cc_start: 0.8780 (mmm) cc_final: 0.8392 (mmm) REVERT: G 144 MET cc_start: 0.9220 (tpt) cc_final: 0.8957 (tpp) REVERT: G 160 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8803 (t) REVERT: G 329 MET cc_start: 0.8259 (mmm) cc_final: 0.7649 (mmm) REVERT: G 379 THR cc_start: 0.8542 (p) cc_final: 0.8331 (t) REVERT: G 548 LEU cc_start: 0.8665 (tp) cc_final: 0.8465 (tp) REVERT: H 68 MET cc_start: 0.6746 (pmm) cc_final: 0.6496 (ttp) REVERT: H 91 MET cc_start: 0.9025 (mpp) cc_final: 0.8796 (mpp) REVERT: H 92 PRO cc_start: 0.8889 (Cg_exo) cc_final: 0.8605 (Cg_endo) REVERT: H 104 PHE cc_start: 0.8970 (t80) cc_final: 0.8627 (t80) REVERT: H 114 TYR cc_start: 0.7403 (m-80) cc_final: 0.7128 (m-80) REVERT: H 172 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6849 (ppp) REVERT: H 183 MET cc_start: 0.8625 (mtt) cc_final: 0.8341 (mtt) REVERT: H 184 MET cc_start: 0.8928 (mmm) cc_final: 0.8525 (mmm) REVERT: H 206 GLU cc_start: 0.8146 (mp0) cc_final: 0.7737 (mp0) REVERT: H 251 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8142 (pt) REVERT: H 254 LEU cc_start: 0.8768 (mt) cc_final: 0.8495 (pp) REVERT: H 258 ASN cc_start: 0.7484 (m-40) cc_final: 0.7278 (m110) REVERT: H 270 PHE cc_start: 0.8285 (m-10) cc_final: 0.8055 (m-10) REVERT: I 94 SER cc_start: 0.9536 (t) cc_final: 0.8701 (t) REVERT: I 149 MET cc_start: 0.9145 (mmm) cc_final: 0.8487 (mtt) REVERT: I 204 ASN cc_start: 0.8775 (m110) cc_final: 0.8472 (t0) REVERT: I 206 GLN cc_start: 0.8185 (tp40) cc_final: 0.7883 (tp40) REVERT: I 209 TYR cc_start: 0.9049 (p90) cc_final: 0.8845 (p90) REVERT: P 133 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7669 (tt0) REVERT: P 134 TRP cc_start: 0.8662 (p90) cc_final: 0.8251 (p90) REVERT: P 217 PHE cc_start: 0.8382 (m-80) cc_final: 0.8037 (m-80) REVERT: P 298 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8072 (t80) REVERT: P 367 GLU cc_start: 0.7632 (mp0) cc_final: 0.7095 (pm20) REVERT: Q 58 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8614 (mmtt) REVERT: Q 85 ASN cc_start: 0.8377 (t0) cc_final: 0.8157 (t0) REVERT: Q 100 GLU cc_start: 0.8177 (tp30) cc_final: 0.7933 (tp30) REVERT: Q 124 MET cc_start: 0.8871 (tpp) cc_final: 0.8544 (mmm) REVERT: Q 160 TYR cc_start: 0.7966 (t80) cc_final: 0.7711 (t80) REVERT: R 110 GLN cc_start: 0.7875 (mp10) cc_final: 0.7487 (mp10) REVERT: T 103 HIS cc_start: 0.8370 (m-70) cc_final: 0.8164 (m90) REVERT: T 113 LEU cc_start: 0.9010 (mp) cc_final: 0.8748 (pt) REVERT: T 115 GLN cc_start: 0.8974 (tt0) cc_final: 0.8434 (tm-30) REVERT: T 117 GLU cc_start: 0.8255 (tm-30) cc_final: 0.6742 (tm-30) REVERT: T 138 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8651 (pp) REVERT: T 139 MET cc_start: 0.6943 (mtt) cc_final: 0.6544 (ttm) REVERT: T 143 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7731 (mt-10) REVERT: V 53 ASN cc_start: 0.9013 (m-40) cc_final: 0.8797 (m-40) REVERT: W 57 ILE cc_start: 0.8583 (pp) cc_final: 0.8323 (pp) REVERT: W 58 THR cc_start: 0.7685 (t) cc_final: 0.7448 (m) REVERT: W 60 LYS cc_start: 0.8806 (ptmt) cc_final: 0.8560 (ptmm) REVERT: W 61 GLN cc_start: 0.7876 (tt0) cc_final: 0.7600 (tt0) REVERT: W 99 VAL cc_start: 0.8392 (t) cc_final: 0.8192 (t) REVERT: W 118 PRO cc_start: 0.8314 (Cg_exo) cc_final: 0.7974 (Cg_endo) REVERT: W 126 TYR cc_start: 0.8736 (m-80) cc_final: 0.8284 (m-80) REVERT: X 47 ARG cc_start: 0.8217 (tpt170) cc_final: 0.6967 (tmt170) REVERT: X 69 ASN cc_start: 0.8968 (t0) cc_final: 0.8552 (t0) REVERT: Z 51 MET cc_start: 0.8098 (tmm) cc_final: 0.7813 (tmm) REVERT: Z 86 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8536 (tp) REVERT: Z 114 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8364 (p) REVERT: Z 137 ASN cc_start: 0.7909 (p0) cc_final: 0.7534 (p0) REVERT: Z 142 TRP cc_start: 0.8184 (m100) cc_final: 0.7479 (m100) REVERT: a 5 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9061 (mm) REVERT: a 61 TYR cc_start: 0.7682 (t80) cc_final: 0.7283 (t80) REVERT: b 11 ASN cc_start: 0.8141 (p0) cc_final: 0.7781 (p0) REVERT: b 43 SER cc_start: 0.9075 (p) cc_final: 0.8728 (m) REVERT: b 47 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8585 (ttpp) REVERT: q 86 TRP cc_start: 0.8510 (m100) cc_final: 0.7965 (m-10) outliers start: 153 outliers final: 79 residues processed: 1079 average time/residue: 0.2025 time to fit residues: 363.8134 Evaluate side-chains 975 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 884 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 368 GLU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 145 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 390 optimal weight: 0.0020 chunk 305 optimal weight: 8.9990 chunk 258 optimal weight: 8.9990 chunk 253 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS F 344 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 171 ASN W 94 GLN X 30 HIS X 64 ASN X 69 ASN Z 76 GLN Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077406 restraints weight = 103312.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080033 restraints weight = 48025.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081785 restraints weight = 28872.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082952 restraints weight = 20409.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083697 restraints weight = 16091.189| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 34709 Z= 0.202 Angle : 0.988 76.394 47099 Z= 0.379 Chirality : 0.046 0.229 5150 Planarity : 0.006 0.128 5975 Dihedral : 8.437 156.893 4792 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.62 % Favored : 95.36 % Rotamer: Outliers : 5.01 % Allowed : 21.15 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4136 helix: 0.22 (0.12), residues: 1839 sheet: -1.34 (0.28), residues: 348 loop : -1.51 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 80 TYR 0.045 0.002 TYR E 112 PHE 0.029 0.002 PHE F 262 TRP 0.027 0.002 TRP A 106 HIS 0.011 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00462 (34668) covalent geometry : angle 0.74206 (47007) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.71003 ( 8) hydrogen bonds : bond 0.04462 ( 1355) hydrogen bonds : angle 5.30853 ( 3849) metal coordination : bond 0.02043 ( 37) metal coordination : angle 15.47473 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 929 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7822 (mtm) cc_final: 0.7544 (mtm) REVERT: A 35 ASN cc_start: 0.8772 (m-40) cc_final: 0.8372 (m-40) REVERT: A 48 ARG cc_start: 0.8247 (tpp80) cc_final: 0.6986 (ptt180) REVERT: A 68 GLU cc_start: 0.8492 (tt0) cc_final: 0.7858 (tt0) REVERT: A 94 LEU cc_start: 0.9039 (tp) cc_final: 0.8364 (tp) REVERT: A 98 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8314 (mm) REVERT: A 113 TRP cc_start: 0.4895 (m100) cc_final: 0.4331 (m100) REVERT: B 103 GLU cc_start: 0.8289 (tp30) cc_final: 0.7582 (tp30) REVERT: B 126 ARG cc_start: 0.8927 (tpp-160) cc_final: 0.8711 (mmt90) REVERT: B 140 LYS cc_start: 0.8457 (mttt) cc_final: 0.8253 (mtmt) REVERT: B 151 GLN cc_start: 0.8830 (mt0) cc_final: 0.8511 (mt0) REVERT: C 103 THR cc_start: 0.9032 (p) cc_final: 0.8607 (p) REVERT: C 106 GLN cc_start: 0.8154 (mp10) cc_final: 0.7643 (mp10) REVERT: C 199 LYS cc_start: 0.9514 (tppt) cc_final: 0.9111 (tppt) REVERT: C 206 TYR cc_start: 0.9165 (m-80) cc_final: 0.8835 (m-80) REVERT: C 216 LYS cc_start: 0.9109 (mptt) cc_final: 0.8871 (mptt) REVERT: D 79 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.7089 (t0) REVERT: D 101 LEU cc_start: 0.9190 (mt) cc_final: 0.8859 (mt) REVERT: D 203 MET cc_start: 0.8644 (mmm) cc_final: 0.8087 (mmm) REVERT: D 212 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 215 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8768 (tm-30) REVERT: E 45 GLU cc_start: 0.8922 (mp0) cc_final: 0.8542 (mp0) REVERT: E 184 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7161 (ptt) REVERT: E 191 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: F 75 TRP cc_start: 0.7592 (t60) cc_final: 0.7000 (t60) REVERT: F 164 ASN cc_start: 0.8071 (p0) cc_final: 0.7595 (t0) REVERT: F 337 MET cc_start: 0.8703 (tpp) cc_final: 0.8499 (tpp) REVERT: G 42 MET cc_start: 0.7062 (tpp) cc_final: 0.6644 (tpp) REVERT: G 117 MET cc_start: 0.8911 (mmm) cc_final: 0.8681 (mmm) REVERT: G 144 MET cc_start: 0.9214 (tpt) cc_final: 0.8938 (tpp) REVERT: G 160 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8869 (t) REVERT: G 254 MET cc_start: 0.8202 (tpp) cc_final: 0.7950 (mpp) REVERT: G 257 VAL cc_start: 0.9416 (OUTLIER) cc_final: 0.9047 (p) REVERT: G 513 MET cc_start: 0.9052 (tpp) cc_final: 0.8625 (tpt) REVERT: G 707 MET cc_start: 0.9189 (mmt) cc_final: 0.8898 (mmp) REVERT: G 712 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8744 (tppt) REVERT: H 47 GLN cc_start: 0.9008 (tp40) cc_final: 0.8508 (tp40) REVERT: H 51 ASP cc_start: 0.9006 (p0) cc_final: 0.8800 (p0) REVERT: H 56 PHE cc_start: 0.8903 (m-10) cc_final: 0.8640 (m-80) REVERT: H 91 MET cc_start: 0.9086 (mpp) cc_final: 0.8834 (mpp) REVERT: H 92 PRO cc_start: 0.8948 (Cg_exo) cc_final: 0.8701 (Cg_endo) REVERT: H 142 TYR cc_start: 0.7322 (m-80) cc_final: 0.6987 (m-80) REVERT: H 183 MET cc_start: 0.8625 (mtt) cc_final: 0.8302 (mtt) REVERT: H 184 MET cc_start: 0.8902 (mmm) cc_final: 0.8204 (mmm) REVERT: H 202 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8134 (tm-30) REVERT: H 206 GLU cc_start: 0.8198 (mp0) cc_final: 0.7446 (mp0) REVERT: H 222 LEU cc_start: 0.9491 (mp) cc_final: 0.9028 (mp) REVERT: H 251 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8149 (pp) REVERT: H 258 ASN cc_start: 0.7601 (m-40) cc_final: 0.7301 (m-40) REVERT: H 282 TYR cc_start: 0.7720 (t80) cc_final: 0.7412 (t80) REVERT: H 285 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8908 (tp) REVERT: H 287 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.8075 (t70) REVERT: H 293 PHE cc_start: 0.8953 (m-10) cc_final: 0.8614 (m-80) REVERT: I 94 SER cc_start: 0.9437 (t) cc_final: 0.8893 (p) REVERT: I 146 ASP cc_start: 0.8143 (m-30) cc_final: 0.7776 (m-30) REVERT: I 200 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8155 (tm-30) REVERT: I 204 ASN cc_start: 0.8756 (m110) cc_final: 0.8424 (t0) REVERT: I 206 GLN cc_start: 0.8214 (tp40) cc_final: 0.7921 (tp40) REVERT: P 97 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7698 (pmm) REVERT: P 133 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7767 (tt0) REVERT: P 134 TRP cc_start: 0.8771 (p90) cc_final: 0.8276 (p90) REVERT: P 298 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8250 (t80) REVERT: P 367 GLU cc_start: 0.7581 (mp0) cc_final: 0.7121 (pm20) REVERT: Q 58 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8523 (mmtt) REVERT: Q 67 VAL cc_start: 0.9000 (t) cc_final: 0.8749 (m) REVERT: Q 112 MET cc_start: 0.8019 (tpt) cc_final: 0.7777 (mmm) REVERT: Q 124 MET cc_start: 0.8957 (tpp) cc_final: 0.8517 (mmm) REVERT: Q 139 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8588 (mm-30) REVERT: R 110 GLN cc_start: 0.7922 (mp10) cc_final: 0.7501 (mp10) REVERT: S 82 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8734 (mt) REVERT: T 103 HIS cc_start: 0.8410 (m-70) cc_final: 0.8197 (m90) REVERT: T 108 LEU cc_start: 0.5650 (mp) cc_final: 0.4988 (tt) REVERT: T 117 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7490 (tm-30) REVERT: T 139 MET cc_start: 0.6528 (mtt) cc_final: 0.6309 (ttm) REVERT: T 142 GLN cc_start: 0.9024 (tt0) cc_final: 0.8778 (mt0) REVERT: T 143 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7691 (mt-10) REVERT: W 45 GLU cc_start: 0.8795 (tp30) cc_final: 0.8255 (tp30) REVERT: W 57 ILE cc_start: 0.8727 (pp) cc_final: 0.8500 (pp) REVERT: W 60 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8686 (ptmm) REVERT: W 94 GLN cc_start: 0.9007 (tt0) cc_final: 0.8769 (tm-30) REVERT: W 99 VAL cc_start: 0.8429 (t) cc_final: 0.8216 (t) REVERT: W 118 PRO cc_start: 0.8258 (Cg_exo) cc_final: 0.7915 (Cg_endo) REVERT: W 126 TYR cc_start: 0.8967 (m-80) cc_final: 0.8547 (m-80) REVERT: X 32 TYR cc_start: 0.9110 (t80) cc_final: 0.8862 (t80) REVERT: X 47 ARG cc_start: 0.8174 (tpt170) cc_final: 0.7009 (tmt170) REVERT: X 69 ASN cc_start: 0.8951 (t0) cc_final: 0.8641 (t0) REVERT: Z 80 ASP cc_start: 0.7929 (m-30) cc_final: 0.7370 (m-30) REVERT: Z 114 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8421 (p) REVERT: a 5 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9137 (mm) REVERT: a 61 TYR cc_start: 0.7748 (t80) cc_final: 0.7396 (t80) REVERT: b 11 ASN cc_start: 0.8152 (p0) cc_final: 0.7838 (p0) REVERT: b 43 SER cc_start: 0.9066 (p) cc_final: 0.8733 (m) REVERT: b 47 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8572 (ttpp) REVERT: q 86 TRP cc_start: 0.8559 (m100) cc_final: 0.7974 (m-10) REVERT: s 90 PHE cc_start: 0.6576 (m-10) cc_final: 0.6352 (m-10) outliers start: 182 outliers final: 107 residues processed: 1036 average time/residue: 0.2122 time to fit residues: 363.9790 Evaluate side-chains 970 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 847 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain W residue 60 LYS Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 64 ASN Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 135 ASN Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 322 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 351 optimal weight: 0.2980 chunk 368 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 356 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN D 92 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 270 ASN ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS F 344 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN H 169 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.077437 restraints weight = 103729.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080086 restraints weight = 48249.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081817 restraints weight = 28768.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.083006 restraints weight = 20288.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083758 restraints weight = 15929.495| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 34709 Z= 0.167 Angle : 0.961 76.433 47099 Z= 0.365 Chirality : 0.045 0.246 5150 Planarity : 0.006 0.128 5975 Dihedral : 8.253 160.745 4792 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 4.32 % Allowed : 22.77 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 4136 helix: 0.38 (0.12), residues: 1841 sheet: -1.33 (0.27), residues: 346 loop : -1.46 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 82 TYR 0.046 0.002 TYR E 112 PHE 0.027 0.002 PHE A 62 TRP 0.017 0.001 TRP A 106 HIS 0.011 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00390 (34668) covalent geometry : angle 0.72105 (47007) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.64319 ( 8) hydrogen bonds : bond 0.04231 ( 1355) hydrogen bonds : angle 5.18189 ( 3849) metal coordination : bond 0.01744 ( 37) metal coordination : angle 15.06420 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 927 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9361 (mt) cc_final: 0.9101 (mp) REVERT: A 35 ASN cc_start: 0.8791 (m-40) cc_final: 0.8519 (m-40) REVERT: A 48 ARG cc_start: 0.8261 (tpp80) cc_final: 0.6909 (ptt180) REVERT: A 55 PHE cc_start: 0.8652 (p90) cc_final: 0.7953 (p90) REVERT: A 68 GLU cc_start: 0.8501 (tt0) cc_final: 0.8128 (tt0) REVERT: A 87 MET cc_start: 0.8565 (tmm) cc_final: 0.8300 (tmm) REVERT: A 94 LEU cc_start: 0.9089 (tp) cc_final: 0.8616 (tp) REVERT: A 98 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 113 TRP cc_start: 0.5232 (m100) cc_final: 0.4677 (m100) REVERT: B 103 GLU cc_start: 0.8268 (tp30) cc_final: 0.7578 (tp30) REVERT: B 151 GLN cc_start: 0.8875 (mt0) cc_final: 0.8477 (mt0) REVERT: C 47 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7496 (tpt170) REVERT: C 103 THR cc_start: 0.9065 (p) cc_final: 0.8674 (p) REVERT: C 106 GLN cc_start: 0.8205 (mp10) cc_final: 0.7642 (mp10) REVERT: C 199 LYS cc_start: 0.9499 (tppt) cc_final: 0.9057 (tppt) REVERT: C 206 TYR cc_start: 0.9157 (m-80) cc_final: 0.8770 (m-80) REVERT: C 216 LYS cc_start: 0.9181 (mptt) cc_final: 0.8881 (mptt) REVERT: D 101 LEU cc_start: 0.9169 (mt) cc_final: 0.8864 (mt) REVERT: D 215 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8702 (tm-30) REVERT: D 443 MET cc_start: 0.7978 (mmt) cc_final: 0.7549 (mmt) REVERT: E 40 HIS cc_start: 0.7643 (t-90) cc_final: 0.7137 (t-90) REVERT: E 184 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7145 (ptt) REVERT: E 191 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: E 205 ASP cc_start: 0.9119 (m-30) cc_final: 0.8894 (p0) REVERT: E 242 PHE cc_start: 0.6599 (t80) cc_final: 0.5900 (t80) REVERT: F 75 TRP cc_start: 0.7639 (t60) cc_final: 0.7062 (t60) REVERT: F 164 ASN cc_start: 0.8080 (p0) cc_final: 0.7600 (t0) REVERT: F 337 MET cc_start: 0.8563 (tpp) cc_final: 0.8338 (tpp) REVERT: F 357 MET cc_start: 0.8014 (ttm) cc_final: 0.7374 (tmm) REVERT: F 450 MET cc_start: 0.8467 (mtt) cc_final: 0.8227 (mtt) REVERT: G 42 MET cc_start: 0.7088 (tpp) cc_final: 0.6693 (tpp) REVERT: G 67 GLU cc_start: 0.8456 (tt0) cc_final: 0.7633 (tm-30) REVERT: G 94 MET cc_start: 0.9183 (tpp) cc_final: 0.8980 (mmm) REVERT: G 117 MET cc_start: 0.8897 (mmm) cc_final: 0.8282 (mmm) REVERT: G 144 MET cc_start: 0.9185 (tpt) cc_final: 0.8950 (tpp) REVERT: G 150 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.8047 (mtt-85) REVERT: G 160 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8862 (t) REVERT: G 239 THR cc_start: 0.9027 (p) cc_final: 0.8807 (t) REVERT: G 257 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9037 (p) REVERT: G 272 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7512 (ttp-110) REVERT: G 277 MET cc_start: 0.8706 (ttp) cc_final: 0.8424 (ttt) REVERT: G 329 MET cc_start: 0.8322 (mmm) cc_final: 0.7745 (mmm) REVERT: G 438 LEU cc_start: 0.8894 (mt) cc_final: 0.8459 (tp) REVERT: G 513 MET cc_start: 0.9019 (tpp) cc_final: 0.8547 (tpt) REVERT: G 605 GLN cc_start: 0.8481 (tt0) cc_final: 0.8060 (tt0) REVERT: G 712 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8733 (tppt) REVERT: H 51 ASP cc_start: 0.8888 (p0) cc_final: 0.8684 (p0) REVERT: H 56 PHE cc_start: 0.8851 (m-10) cc_final: 0.8628 (m-80) REVERT: H 91 MET cc_start: 0.9104 (mpp) cc_final: 0.8815 (mpp) REVERT: H 92 PRO cc_start: 0.8877 (Cg_exo) cc_final: 0.8599 (Cg_endo) REVERT: H 172 MET cc_start: 0.7780 (tmm) cc_final: 0.7335 (tmm) REVERT: H 183 MET cc_start: 0.8663 (mtt) cc_final: 0.8377 (mtt) REVERT: H 184 MET cc_start: 0.8932 (mmm) cc_final: 0.8633 (mmm) REVERT: H 202 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8111 (tm-30) REVERT: H 206 GLU cc_start: 0.8150 (mp0) cc_final: 0.7663 (mp0) REVERT: H 222 LEU cc_start: 0.9479 (mp) cc_final: 0.9032 (mp) REVERT: H 258 ASN cc_start: 0.7728 (m-40) cc_final: 0.6971 (m-40) REVERT: H 279 ARG cc_start: 0.7104 (ptm160) cc_final: 0.6880 (ptp90) REVERT: I 94 SER cc_start: 0.9409 (t) cc_final: 0.8883 (p) REVERT: I 146 ASP cc_start: 0.7965 (m-30) cc_final: 0.7755 (m-30) REVERT: I 204 ASN cc_start: 0.8767 (m110) cc_final: 0.8428 (t0) REVERT: I 206 GLN cc_start: 0.8313 (tp40) cc_final: 0.8081 (tp-100) REVERT: P 97 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7677 (pmm) REVERT: P 133 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7802 (tt0) REVERT: P 134 TRP cc_start: 0.8764 (p90) cc_final: 0.8267 (p90) REVERT: P 298 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8418 (t80) REVERT: P 367 GLU cc_start: 0.7371 (mp0) cc_final: 0.7079 (pm20) REVERT: Q 67 VAL cc_start: 0.9002 (t) cc_final: 0.8748 (m) REVERT: Q 101 PHE cc_start: 0.8150 (m-80) cc_final: 0.7916 (m-80) REVERT: R 110 GLN cc_start: 0.7871 (mp10) cc_final: 0.7397 (mp10) REVERT: T 90 TYR cc_start: 0.7429 (t80) cc_final: 0.6833 (t80) REVERT: T 103 HIS cc_start: 0.8445 (m-70) cc_final: 0.8203 (m90) REVERT: T 108 LEU cc_start: 0.5665 (mp) cc_final: 0.4977 (tt) REVERT: T 115 GLN cc_start: 0.8853 (tt0) cc_final: 0.8157 (tm-30) REVERT: T 117 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7474 (tm-30) REVERT: T 142 GLN cc_start: 0.8955 (tt0) cc_final: 0.8647 (mt0) REVERT: W 45 GLU cc_start: 0.8838 (tp30) cc_final: 0.8152 (tp30) REVERT: W 60 LYS cc_start: 0.8918 (ptmt) cc_final: 0.8570 (ptmm) REVERT: W 118 PRO cc_start: 0.8250 (Cg_exo) cc_final: 0.7925 (Cg_endo) REVERT: W 126 TYR cc_start: 0.9045 (m-80) cc_final: 0.8636 (m-80) REVERT: X 32 TYR cc_start: 0.9171 (t80) cc_final: 0.8937 (t80) REVERT: X 47 ARG cc_start: 0.8242 (tpt170) cc_final: 0.7059 (tpt90) REVERT: Z 45 PHE cc_start: 0.8960 (t80) cc_final: 0.8620 (t80) REVERT: Z 80 ASP cc_start: 0.7892 (m-30) cc_final: 0.7369 (m-30) REVERT: Z 114 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8440 (p) REVERT: a 5 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9121 (mm) REVERT: a 61 TYR cc_start: 0.7823 (t80) cc_final: 0.7397 (t80) REVERT: b 11 ASN cc_start: 0.8139 (p0) cc_final: 0.7835 (p0) REVERT: b 43 SER cc_start: 0.9054 (p) cc_final: 0.8762 (m) REVERT: b 47 LYS cc_start: 0.8821 (ttpp) cc_final: 0.8565 (ttpp) REVERT: q 86 TRP cc_start: 0.8558 (m100) cc_final: 0.7944 (m100) REVERT: s 90 PHE cc_start: 0.6700 (m-10) cc_final: 0.6480 (m-10) outliers start: 157 outliers final: 105 residues processed: 1017 average time/residue: 0.2080 time to fit residues: 351.7181 Evaluate side-chains 975 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 860 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 95 optimal weight: 0.0020 chunk 133 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 317 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 309 optimal weight: 7.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 92 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS F 344 GLN F 436 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN I 204 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN Z 76 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.077213 restraints weight = 102891.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.079813 restraints weight = 47973.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081552 restraints weight = 28797.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082723 restraints weight = 20354.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083412 restraints weight = 16036.765| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34709 Z= 0.159 Angle : 0.959 76.650 47099 Z= 0.363 Chirality : 0.045 0.246 5150 Planarity : 0.006 0.129 5975 Dihedral : 8.150 163.571 4792 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 4.51 % Allowed : 23.38 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 4136 helix: 0.51 (0.12), residues: 1837 sheet: -1.38 (0.27), residues: 357 loop : -1.38 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 82 TYR 0.050 0.002 TYR E 112 PHE 0.028 0.002 PHE A 62 TRP 0.016 0.001 TRP A 106 HIS 0.010 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00374 (34668) covalent geometry : angle 0.72145 (47007) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.65225 ( 8) hydrogen bonds : bond 0.04036 ( 1355) hydrogen bonds : angle 5.11660 ( 3849) metal coordination : bond 0.01726 ( 37) metal coordination : angle 14.98467 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 916 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8786 (m-40) cc_final: 0.8564 (m-40) REVERT: A 48 ARG cc_start: 0.8414 (tpp80) cc_final: 0.6863 (ptt180) REVERT: A 87 MET cc_start: 0.8634 (tmm) cc_final: 0.8162 (tmm) REVERT: A 94 LEU cc_start: 0.9135 (tp) cc_final: 0.8726 (tp) REVERT: A 98 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8103 (mm) REVERT: B 103 GLU cc_start: 0.8248 (tp30) cc_final: 0.7554 (tp30) REVERT: B 173 TYR cc_start: 0.8729 (m-80) cc_final: 0.8494 (m-80) REVERT: C 47 ARG cc_start: 0.7918 (mmm160) cc_final: 0.7546 (tpt170) REVERT: C 103 THR cc_start: 0.9119 (p) cc_final: 0.8757 (p) REVERT: C 106 GLN cc_start: 0.8335 (mp10) cc_final: 0.7770 (mp10) REVERT: C 199 LYS cc_start: 0.9535 (tppt) cc_final: 0.9082 (tppp) REVERT: C 206 TYR cc_start: 0.9150 (m-80) cc_final: 0.8772 (m-80) REVERT: C 216 LYS cc_start: 0.9190 (mptt) cc_final: 0.8844 (mptt) REVERT: D 121 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7989 (mp0) REVERT: D 203 MET cc_start: 0.8668 (mmm) cc_final: 0.8076 (mmm) REVERT: D 414 ASP cc_start: 0.8302 (m-30) cc_final: 0.7940 (m-30) REVERT: D 443 MET cc_start: 0.7877 (mmt) cc_final: 0.7493 (mmt) REVERT: D 454 GLN cc_start: 0.8484 (mt0) cc_final: 0.8250 (mt0) REVERT: E 40 HIS cc_start: 0.7858 (t-90) cc_final: 0.7483 (t-90) REVERT: E 184 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7272 (ptp) REVERT: E 191 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: F 75 TRP cc_start: 0.7677 (t60) cc_final: 0.7326 (t60) REVERT: F 164 ASN cc_start: 0.8060 (p0) cc_final: 0.7501 (t0) REVERT: F 337 MET cc_start: 0.8591 (tpp) cc_final: 0.8338 (tpp) REVERT: F 357 MET cc_start: 0.8076 (ttm) cc_final: 0.7521 (tmm) REVERT: G 42 MET cc_start: 0.7198 (tpp) cc_final: 0.6894 (tpp) REVERT: G 67 GLU cc_start: 0.8290 (tt0) cc_final: 0.7622 (tm-30) REVERT: G 117 MET cc_start: 0.9016 (mmm) cc_final: 0.8340 (mmm) REVERT: G 150 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.8039 (mtt-85) REVERT: G 160 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8960 (t) REVERT: G 217 GLU cc_start: 0.7780 (pm20) cc_final: 0.7467 (pm20) REVERT: G 239 THR cc_start: 0.8990 (p) cc_final: 0.8749 (t) REVERT: G 257 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9026 (p) REVERT: G 277 MET cc_start: 0.8692 (ttp) cc_final: 0.8437 (ttt) REVERT: G 283 GLU cc_start: 0.7914 (pm20) cc_final: 0.6941 (pt0) REVERT: G 438 LEU cc_start: 0.8927 (mt) cc_final: 0.8506 (tp) REVERT: G 513 MET cc_start: 0.9013 (tpp) cc_final: 0.8604 (tpt) REVERT: G 605 GLN cc_start: 0.8483 (tt0) cc_final: 0.8130 (tt0) REVERT: G 707 MET cc_start: 0.9115 (mmt) cc_final: 0.8843 (mmp) REVERT: G 712 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8732 (tppt) REVERT: H 17 MET cc_start: 0.9066 (tmm) cc_final: 0.8856 (tmm) REVERT: H 35 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8311 (tptt) REVERT: H 92 PRO cc_start: 0.8794 (Cg_exo) cc_final: 0.8549 (Cg_endo) REVERT: H 126 LYS cc_start: 0.8004 (ptpp) cc_final: 0.7542 (pttp) REVERT: H 172 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7297 (tmm) REVERT: H 183 MET cc_start: 0.8630 (mtt) cc_final: 0.8201 (mtp) REVERT: H 184 MET cc_start: 0.8938 (mmm) cc_final: 0.8658 (mmm) REVERT: H 202 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8153 (tm-30) REVERT: H 206 GLU cc_start: 0.8136 (mp0) cc_final: 0.7441 (mp0) REVERT: H 261 MET cc_start: 0.8522 (mmm) cc_final: 0.8230 (mmt) REVERT: H 279 ARG cc_start: 0.7054 (ptm160) cc_final: 0.6622 (ptm160) REVERT: H 287 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.8098 (t70) REVERT: H 302 MET cc_start: 0.8990 (ttt) cc_final: 0.8759 (ttt) REVERT: I 94 SER cc_start: 0.9419 (t) cc_final: 0.8843 (p) REVERT: I 128 ILE cc_start: 0.8318 (mm) cc_final: 0.8024 (mm) REVERT: I 204 ASN cc_start: 0.8836 (m-40) cc_final: 0.8453 (t0) REVERT: I 206 GLN cc_start: 0.8314 (tp40) cc_final: 0.8086 (tp-100) REVERT: P 97 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7746 (pmm) REVERT: P 133 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7892 (tt0) REVERT: P 134 TRP cc_start: 0.8813 (p90) cc_final: 0.8366 (p90) REVERT: P 181 LEU cc_start: 0.9401 (mt) cc_final: 0.9192 (mp) REVERT: P 298 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8481 (t80) REVERT: P 360 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8320 (tmt-80) REVERT: P 367 GLU cc_start: 0.7365 (mp0) cc_final: 0.7139 (pm20) REVERT: Q 58 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7764 (ptpp) REVERT: Q 67 VAL cc_start: 0.9008 (t) cc_final: 0.8738 (m) REVERT: Q 148 GLU cc_start: 0.8195 (tp30) cc_final: 0.7725 (mt-10) REVERT: R 110 GLN cc_start: 0.7882 (mp10) cc_final: 0.7414 (mp10) REVERT: T 103 HIS cc_start: 0.8427 (m-70) cc_final: 0.8181 (m90) REVERT: T 108 LEU cc_start: 0.5767 (mp) cc_final: 0.5100 (tt) REVERT: T 115 GLN cc_start: 0.8789 (tt0) cc_final: 0.8176 (tm-30) REVERT: T 117 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7436 (tm-30) REVERT: T 143 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7545 (mp0) REVERT: V 58 MET cc_start: 0.7965 (ptp) cc_final: 0.7743 (ptp) REVERT: V 85 GLU cc_start: 0.8646 (pp20) cc_final: 0.8122 (pt0) REVERT: W 45 GLU cc_start: 0.8911 (tp30) cc_final: 0.8090 (tp30) REVERT: W 52 LEU cc_start: 0.9352 (tp) cc_final: 0.9144 (tt) REVERT: W 53 MET cc_start: 0.8840 (tpp) cc_final: 0.8518 (tpp) REVERT: W 118 PRO cc_start: 0.8263 (Cg_exo) cc_final: 0.7936 (Cg_endo) REVERT: W 126 TYR cc_start: 0.9142 (m-80) cc_final: 0.8781 (m-80) REVERT: X 47 ARG cc_start: 0.8201 (tpt170) cc_final: 0.7084 (tpt90) REVERT: X 50 GLU cc_start: 0.8360 (tt0) cc_final: 0.8141 (tt0) REVERT: Z 98 MET cc_start: 0.1964 (tpt) cc_final: 0.1600 (tpt) REVERT: Z 114 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8416 (p) REVERT: Z 137 ASN cc_start: 0.7913 (p0) cc_final: 0.7699 (p0) REVERT: a 5 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9081 (mm) REVERT: a 61 TYR cc_start: 0.7877 (t80) cc_final: 0.7405 (t80) REVERT: b 11 ASN cc_start: 0.8110 (p0) cc_final: 0.7840 (p0) REVERT: b 43 SER cc_start: 0.9038 (p) cc_final: 0.8807 (m) REVERT: q 86 TRP cc_start: 0.8562 (m100) cc_final: 0.7887 (m100) REVERT: s 90 PHE cc_start: 0.6843 (m-10) cc_final: 0.6578 (m-80) outliers start: 164 outliers final: 108 residues processed: 1003 average time/residue: 0.2113 time to fit residues: 351.7184 Evaluate side-chains 976 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 854 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 266 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 360 ARG Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 137 LYS Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain s residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 398 optimal weight: 30.0000 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 41 optimal weight: 0.0980 chunk 143 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 326 optimal weight: 8.9990 chunk 314 optimal weight: 8.9990 chunk 360 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN D 79 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 ASN S 48 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076043 restraints weight = 104203.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078617 restraints weight = 48539.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080328 restraints weight = 29170.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081500 restraints weight = 20673.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082252 restraints weight = 16284.379| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34709 Z= 0.183 Angle : 0.982 78.379 47099 Z= 0.372 Chirality : 0.046 0.277 5150 Planarity : 0.006 0.130 5975 Dihedral : 8.085 168.307 4792 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 4.51 % Allowed : 24.09 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 4136 helix: 0.53 (0.12), residues: 1840 sheet: -1.39 (0.28), residues: 346 loop : -1.31 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P 150 TYR 0.050 0.002 TYR E 112 PHE 0.031 0.002 PHE A 55 TRP 0.018 0.001 TRP a 2 HIS 0.007 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00427 (34668) covalent geometry : angle 0.73598 (47007) SS BOND : bond 0.00228 ( 4) SS BOND : angle 0.66329 ( 8) hydrogen bonds : bond 0.04063 ( 1355) hydrogen bonds : angle 5.13958 ( 3849) metal coordination : bond 0.01972 ( 37) metal coordination : angle 15.39630 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 898 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8521 (tpp80) cc_final: 0.6899 (ptt180) REVERT: A 68 GLU cc_start: 0.8348 (tt0) cc_final: 0.7517 (tt0) REVERT: A 83 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8672 (mmmt) REVERT: A 94 LEU cc_start: 0.8960 (tp) cc_final: 0.8556 (tp) REVERT: A 98 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8506 (mm) REVERT: B 103 GLU cc_start: 0.8296 (tp30) cc_final: 0.7685 (tp30) REVERT: C 47 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7562 (tpt170) REVERT: C 199 LYS cc_start: 0.9517 (tppt) cc_final: 0.9007 (tppp) REVERT: C 206 TYR cc_start: 0.9141 (m-80) cc_final: 0.8815 (m-80) REVERT: C 216 LYS cc_start: 0.9145 (mptt) cc_final: 0.8810 (mptt) REVERT: D 145 MET cc_start: 0.8681 (mtt) cc_final: 0.8481 (mtt) REVERT: D 203 MET cc_start: 0.8779 (mmm) cc_final: 0.8105 (mmm) REVERT: D 215 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8546 (tm-30) REVERT: D 300 TRP cc_start: 0.9036 (t-100) cc_final: 0.8829 (t-100) REVERT: D 414 ASP cc_start: 0.8307 (m-30) cc_final: 0.7985 (m-30) REVERT: D 443 MET cc_start: 0.7927 (mmt) cc_final: 0.7531 (mmt) REVERT: D 454 GLN cc_start: 0.8490 (mt0) cc_final: 0.8272 (mt0) REVERT: E 40 HIS cc_start: 0.8030 (t-90) cc_final: 0.7548 (t-90) REVERT: E 59 TYR cc_start: 0.8272 (m-80) cc_final: 0.7983 (m-80) REVERT: E 184 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7290 (ptp) REVERT: E 191 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: E 205 ASP cc_start: 0.9199 (m-30) cc_final: 0.8899 (p0) REVERT: F 75 TRP cc_start: 0.7831 (t60) cc_final: 0.7302 (t60) REVERT: F 164 ASN cc_start: 0.8069 (p0) cc_final: 0.7475 (t0) REVERT: F 337 MET cc_start: 0.8598 (tpp) cc_final: 0.8398 (tpp) REVERT: F 357 MET cc_start: 0.8193 (ttm) cc_final: 0.7694 (tmm) REVERT: G 42 MET cc_start: 0.7234 (tpp) cc_final: 0.7024 (tpp) REVERT: G 67 GLU cc_start: 0.8312 (tt0) cc_final: 0.7676 (tm-30) REVERT: G 94 MET cc_start: 0.9153 (mmm) cc_final: 0.8886 (tpt) REVERT: G 117 MET cc_start: 0.8961 (mmm) cc_final: 0.8391 (mmm) REVERT: G 150 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.8023 (mtt-85) REVERT: G 160 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8977 (t) REVERT: G 217 GLU cc_start: 0.7806 (pm20) cc_final: 0.7495 (pm20) REVERT: G 239 THR cc_start: 0.8961 (p) cc_final: 0.8698 (t) REVERT: G 269 GLU cc_start: 0.7555 (pm20) cc_final: 0.7088 (pm20) REVERT: G 277 MET cc_start: 0.8672 (ttp) cc_final: 0.8398 (ttt) REVERT: G 707 MET cc_start: 0.9161 (mmt) cc_final: 0.8891 (mmp) REVERT: G 712 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8721 (tppt) REVERT: H 92 PRO cc_start: 0.8821 (Cg_exo) cc_final: 0.8602 (Cg_endo) REVERT: H 143 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8211 (mt-10) REVERT: H 172 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7553 (tmm) REVERT: H 183 MET cc_start: 0.8647 (mtt) cc_final: 0.8283 (mtp) REVERT: H 202 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8063 (tm-30) REVERT: H 206 GLU cc_start: 0.8117 (mp0) cc_final: 0.7752 (mp0) REVERT: H 228 TYR cc_start: 0.8858 (m-80) cc_final: 0.8580 (m-80) REVERT: H 261 MET cc_start: 0.8591 (mmm) cc_final: 0.8341 (mtt) REVERT: H 279 ARG cc_start: 0.7595 (ptm160) cc_final: 0.7292 (ptm160) REVERT: H 302 MET cc_start: 0.9113 (ttt) cc_final: 0.8907 (ttt) REVERT: I 94 SER cc_start: 0.9492 (t) cc_final: 0.8893 (p) REVERT: I 128 ILE cc_start: 0.8448 (mm) cc_final: 0.8222 (mm) REVERT: I 200 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8107 (tm-30) REVERT: I 204 ASN cc_start: 0.8848 (m-40) cc_final: 0.8467 (t0) REVERT: I 206 GLN cc_start: 0.8347 (tp40) cc_final: 0.8029 (tp-100) REVERT: P 97 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7901 (pmm) REVERT: P 133 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7875 (tt0) REVERT: P 134 TRP cc_start: 0.8841 (p90) cc_final: 0.8421 (p90) REVERT: P 181 LEU cc_start: 0.9467 (mt) cc_final: 0.9261 (mp) REVERT: P 296 PHE cc_start: 0.8700 (p90) cc_final: 0.8470 (p90) REVERT: P 298 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8533 (t80) REVERT: P 360 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8365 (tmt-80) REVERT: Q 67 VAL cc_start: 0.9004 (t) cc_final: 0.8795 (m) REVERT: R 110 GLN cc_start: 0.7888 (mp10) cc_final: 0.7460 (mp10) REVERT: T 90 TYR cc_start: 0.7357 (t80) cc_final: 0.6098 (t80) REVERT: T 108 LEU cc_start: 0.5715 (mp) cc_final: 0.4975 (tt) REVERT: T 115 GLN cc_start: 0.8863 (tt0) cc_final: 0.8212 (tm-30) REVERT: T 117 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7672 (tm-30) REVERT: W 45 GLU cc_start: 0.8905 (tp30) cc_final: 0.8052 (tp30) REVERT: W 118 PRO cc_start: 0.8281 (Cg_exo) cc_final: 0.8032 (Cg_endo) REVERT: W 124 LYS cc_start: 0.8775 (tptt) cc_final: 0.8050 (tptt) REVERT: W 126 TYR cc_start: 0.9221 (m-80) cc_final: 0.8822 (m-80) REVERT: X 37 ASP cc_start: 0.6908 (p0) cc_final: 0.5909 (p0) REVERT: X 47 ARG cc_start: 0.8138 (tpt170) cc_final: 0.7093 (tpt90) REVERT: X 50 GLU cc_start: 0.8387 (tt0) cc_final: 0.8174 (tt0) REVERT: Z 86 ILE cc_start: 0.8968 (mm) cc_final: 0.8727 (tt) REVERT: Z 98 MET cc_start: 0.1938 (tpt) cc_final: 0.1592 (tpt) REVERT: a 5 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9146 (mm) REVERT: a 61 TYR cc_start: 0.7940 (t80) cc_final: 0.7289 (t80) REVERT: b 11 ASN cc_start: 0.8119 (p0) cc_final: 0.7860 (p0) REVERT: b 43 SER cc_start: 0.9089 (p) cc_final: 0.8795 (m) REVERT: b 47 LYS cc_start: 0.9360 (tptt) cc_final: 0.8810 (ttpp) REVERT: q 86 TRP cc_start: 0.8685 (m100) cc_final: 0.8009 (m100) REVERT: q 132 LYS cc_start: 0.8464 (tttp) cc_final: 0.8156 (ptmm) REVERT: s 84 ASN cc_start: 0.8302 (m110) cc_final: 0.7225 (t0) outliers start: 164 outliers final: 122 residues processed: 980 average time/residue: 0.2129 time to fit residues: 345.8261 Evaluate side-chains 964 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 832 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 266 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 360 ARG Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 139 MET Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain s residue 85 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 245 optimal weight: 1.9990 chunk 402 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 390 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 270 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 ASN Z 76 GLN a 31 ASN a 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.077476 restraints weight = 102951.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080019 restraints weight = 49654.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081695 restraints weight = 30287.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082742 restraints weight = 21640.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083517 restraints weight = 17484.321| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 34709 Z= 0.149 Angle : 0.965 77.166 47099 Z= 0.369 Chirality : 0.045 0.260 5150 Planarity : 0.006 0.130 5975 Dihedral : 7.982 168.948 4792 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.79 % Favored : 95.19 % Rotamer: Outliers : 3.88 % Allowed : 24.83 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 4136 helix: 0.47 (0.12), residues: 1854 sheet: -1.28 (0.28), residues: 348 loop : -1.30 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 82 TYR 0.049 0.002 TYR E 112 PHE 0.031 0.002 PHE A 55 TRP 0.019 0.001 TRP V 114 HIS 0.010 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00350 (34668) covalent geometry : angle 0.73947 (47007) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.64323 ( 8) hydrogen bonds : bond 0.03960 ( 1355) hydrogen bonds : angle 5.08100 ( 3849) metal coordination : bond 0.01574 ( 37) metal coordination : angle 14.69622 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 910 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8463 (tpp80) cc_final: 0.6739 (ptt180) REVERT: A 68 GLU cc_start: 0.8536 (tt0) cc_final: 0.8190 (tt0) REVERT: B 103 GLU cc_start: 0.8322 (tp30) cc_final: 0.7893 (tp30) REVERT: C 47 ARG cc_start: 0.7901 (mmm160) cc_final: 0.7544 (tpt170) REVERT: C 106 GLN cc_start: 0.8490 (mp10) cc_final: 0.7866 (mp10) REVERT: C 108 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8711 (mmmt) REVERT: C 199 LYS cc_start: 0.9493 (tppt) cc_final: 0.8990 (tppp) REVERT: C 206 TYR cc_start: 0.9148 (m-80) cc_final: 0.8845 (m-80) REVERT: C 216 LYS cc_start: 0.9163 (mptt) cc_final: 0.8801 (mptt) REVERT: D 105 MET cc_start: 0.7955 (mmm) cc_final: 0.7681 (mmm) REVERT: D 203 MET cc_start: 0.8683 (mmm) cc_final: 0.8146 (mmt) REVERT: D 204 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8301 (m-10) REVERT: D 210 MET cc_start: 0.8726 (mtm) cc_final: 0.8270 (mpp) REVERT: D 215 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8565 (tm-30) REVERT: D 414 ASP cc_start: 0.8210 (m-30) cc_final: 0.7903 (m-30) REVERT: D 443 MET cc_start: 0.7743 (mmt) cc_final: 0.7374 (mmt) REVERT: D 454 GLN cc_start: 0.8401 (mt0) cc_final: 0.7990 (mt0) REVERT: E 52 PHE cc_start: 0.8040 (t80) cc_final: 0.7710 (t80) REVERT: E 59 TYR cc_start: 0.8360 (m-80) cc_final: 0.7951 (m-80) REVERT: E 83 ASP cc_start: 0.9385 (t0) cc_final: 0.8587 (t0) REVERT: E 122 ASN cc_start: 0.8335 (m-40) cc_final: 0.6627 (t0) REVERT: E 184 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7252 (ptt) REVERT: E 191 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: E 205 ASP cc_start: 0.9183 (m-30) cc_final: 0.8926 (p0) REVERT: F 75 TRP cc_start: 0.7837 (t60) cc_final: 0.7276 (t60) REVERT: F 163 TYR cc_start: 0.7548 (t80) cc_final: 0.7257 (t80) REVERT: F 164 ASN cc_start: 0.7765 (p0) cc_final: 0.7265 (t0) REVERT: F 337 MET cc_start: 0.8482 (tpp) cc_final: 0.8241 (tpp) REVERT: F 349 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6690 (tp) REVERT: F 357 MET cc_start: 0.8245 (ttm) cc_final: 0.7670 (tmm) REVERT: G 42 MET cc_start: 0.7247 (tpp) cc_final: 0.7045 (tpp) REVERT: G 67 GLU cc_start: 0.8275 (tt0) cc_final: 0.7650 (tm-30) REVERT: G 117 MET cc_start: 0.9023 (mmm) cc_final: 0.8430 (mmm) REVERT: G 160 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8891 (t) REVERT: G 217 GLU cc_start: 0.7709 (pm20) cc_final: 0.7420 (pm20) REVERT: G 239 THR cc_start: 0.8982 (p) cc_final: 0.8695 (t) REVERT: G 269 GLU cc_start: 0.7518 (pm20) cc_final: 0.7058 (pm20) REVERT: G 277 MET cc_start: 0.8630 (ttp) cc_final: 0.8374 (ttt) REVERT: G 283 GLU cc_start: 0.7898 (pm20) cc_final: 0.7056 (pt0) REVERT: G 329 MET cc_start: 0.8429 (mmm) cc_final: 0.7700 (mmm) REVERT: G 438 LEU cc_start: 0.8975 (mt) cc_final: 0.8535 (tp) REVERT: G 605 GLN cc_start: 0.8461 (tt0) cc_final: 0.8063 (tt0) REVERT: G 707 MET cc_start: 0.9158 (mmt) cc_final: 0.8879 (mmp) REVERT: G 712 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8887 (tppt) REVERT: H 92 PRO cc_start: 0.8816 (Cg_exo) cc_final: 0.8580 (Cg_endo) REVERT: H 143 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8244 (mt-10) REVERT: H 172 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7478 (tmm) REVERT: H 173 TRP cc_start: 0.7572 (m-10) cc_final: 0.6923 (m-90) REVERT: H 183 MET cc_start: 0.8592 (mtt) cc_final: 0.8136 (mtp) REVERT: H 202 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8153 (tm-30) REVERT: H 206 GLU cc_start: 0.8067 (mp0) cc_final: 0.7646 (mp0) REVERT: H 228 TYR cc_start: 0.8807 (m-80) cc_final: 0.8598 (m-80) REVERT: H 279 ARG cc_start: 0.7558 (ptm160) cc_final: 0.7149 (ptm160) REVERT: H 291 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8750 (mtpp) REVERT: H 302 MET cc_start: 0.9065 (ttt) cc_final: 0.8551 (ttt) REVERT: I 94 SER cc_start: 0.9491 (t) cc_final: 0.8888 (p) REVERT: I 204 ASN cc_start: 0.8819 (m-40) cc_final: 0.8523 (t0) REVERT: I 206 GLN cc_start: 0.8269 (tp40) cc_final: 0.7939 (tp-100) REVERT: P 97 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7891 (pmm) REVERT: P 133 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7917 (tt0) REVERT: P 134 TRP cc_start: 0.8814 (p90) cc_final: 0.8380 (p90) REVERT: P 174 MET cc_start: 0.8600 (mmm) cc_final: 0.8310 (mmp) REVERT: P 296 PHE cc_start: 0.8719 (p90) cc_final: 0.8499 (p90) REVERT: P 298 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8500 (t80) REVERT: P 360 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8342 (tmt-80) REVERT: Q 69 GLU cc_start: 0.7980 (pm20) cc_final: 0.7736 (pm20) REVERT: Q 145 TYR cc_start: 0.8748 (p90) cc_final: 0.8540 (p90) REVERT: R 110 GLN cc_start: 0.7753 (mp10) cc_final: 0.7375 (mp10) REVERT: T 82 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8076 (mtp180) REVERT: T 108 LEU cc_start: 0.5734 (mp) cc_final: 0.4982 (tt) REVERT: T 115 GLN cc_start: 0.8900 (tt0) cc_final: 0.8517 (tm-30) REVERT: T 117 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8074 (tm-30) REVERT: V 85 GLU cc_start: 0.8672 (pp20) cc_final: 0.8209 (pt0) REVERT: W 45 GLU cc_start: 0.8945 (tp30) cc_final: 0.8077 (tp30) REVERT: W 118 PRO cc_start: 0.8248 (Cg_exo) cc_final: 0.7988 (Cg_endo) REVERT: W 124 LYS cc_start: 0.8757 (tptt) cc_final: 0.8037 (tptt) REVERT: W 126 TYR cc_start: 0.9225 (m-80) cc_final: 0.8895 (m-80) REVERT: X 26 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8814 (ttpt) REVERT: X 37 ASP cc_start: 0.6935 (p0) cc_final: 0.5952 (p0) REVERT: X 47 ARG cc_start: 0.8048 (tpt170) cc_final: 0.7073 (tpt90) REVERT: Z 98 MET cc_start: 0.1922 (tpt) cc_final: 0.1693 (tpt) REVERT: Z 133 MET cc_start: 0.7606 (tpt) cc_final: 0.7386 (tpt) REVERT: a 5 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9133 (mm) REVERT: a 48 MET cc_start: 0.8791 (mmm) cc_final: 0.8457 (mmm) REVERT: a 61 TYR cc_start: 0.7846 (t80) cc_final: 0.7366 (t80) REVERT: b 43 SER cc_start: 0.9085 (p) cc_final: 0.8790 (m) REVERT: b 47 LYS cc_start: 0.9238 (tptt) cc_final: 0.8633 (ttpp) REVERT: q 86 TRP cc_start: 0.8702 (m100) cc_final: 0.8022 (m100) outliers start: 141 outliers final: 105 residues processed: 988 average time/residue: 0.2107 time to fit residues: 345.3384 Evaluate side-chains 963 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 847 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 266 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 360 ARG Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 137 LYS Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 339 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 336 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 chunk 406 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077219 restraints weight = 102632.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.079739 restraints weight = 49396.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.081420 restraints weight = 30171.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082520 restraints weight = 21562.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083259 restraints weight = 17262.177| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.7016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 34709 Z= 0.157 Angle : 0.978 77.595 47099 Z= 0.376 Chirality : 0.045 0.261 5150 Planarity : 0.006 0.131 5975 Dihedral : 7.937 169.602 4792 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 3.80 % Allowed : 25.30 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4136 helix: 0.51 (0.12), residues: 1858 sheet: -1.32 (0.28), residues: 348 loop : -1.29 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 82 TYR 0.054 0.002 TYR E 112 PHE 0.030 0.002 PHE A 62 TRP 0.052 0.002 TRP b 80 HIS 0.008 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00374 (34668) covalent geometry : angle 0.75408 (47007) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.88128 ( 8) hydrogen bonds : bond 0.03956 ( 1355) hydrogen bonds : angle 5.09084 ( 3849) metal coordination : bond 0.01558 ( 37) metal coordination : angle 14.76950 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 878 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8413 (tpp80) cc_final: 0.6658 (ptt180) REVERT: A 106 TRP cc_start: 0.7707 (t60) cc_final: 0.7502 (t60) REVERT: B 103 GLU cc_start: 0.8329 (tp30) cc_final: 0.8018 (tp30) REVERT: C 47 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7589 (tpt170) REVERT: C 108 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8724 (mmmt) REVERT: C 199 LYS cc_start: 0.9488 (tppt) cc_final: 0.8978 (tppp) REVERT: C 216 LYS cc_start: 0.9170 (tptt) cc_final: 0.8804 (mptt) REVERT: D 105 MET cc_start: 0.8034 (mmm) cc_final: 0.7814 (mmm) REVERT: D 121 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8003 (mp0) REVERT: D 185 MET cc_start: 0.9302 (tpt) cc_final: 0.8684 (tpp) REVERT: D 203 MET cc_start: 0.8745 (mmm) cc_final: 0.8136 (mmt) REVERT: D 204 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8385 (m-10) REVERT: D 215 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 414 ASP cc_start: 0.8172 (m-30) cc_final: 0.7924 (m-30) REVERT: D 443 MET cc_start: 0.7652 (mmt) cc_final: 0.7283 (mmt) REVERT: E 59 TYR cc_start: 0.8374 (m-80) cc_final: 0.7931 (m-80) REVERT: E 122 ASN cc_start: 0.8251 (m-40) cc_final: 0.6655 (t0) REVERT: E 184 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7259 (ptt) REVERT: E 191 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: E 205 ASP cc_start: 0.9152 (m-30) cc_final: 0.8909 (p0) REVERT: F 75 TRP cc_start: 0.7829 (t60) cc_final: 0.7278 (t60) REVERT: F 163 TYR cc_start: 0.7593 (t80) cc_final: 0.7290 (t80) REVERT: F 164 ASN cc_start: 0.7733 (p0) cc_final: 0.7254 (t0) REVERT: F 337 MET cc_start: 0.8505 (tpp) cc_final: 0.8265 (tpp) REVERT: F 349 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6694 (tp) REVERT: F 357 MET cc_start: 0.8115 (ttm) cc_final: 0.7346 (tmm) REVERT: G 67 GLU cc_start: 0.8255 (tt0) cc_final: 0.7640 (tm-30) REVERT: G 117 MET cc_start: 0.8992 (mmm) cc_final: 0.8458 (mmm) REVERT: G 160 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8913 (t) REVERT: G 217 GLU cc_start: 0.7677 (pm20) cc_final: 0.7380 (pm20) REVERT: G 239 THR cc_start: 0.8982 (p) cc_final: 0.8691 (t) REVERT: G 269 GLU cc_start: 0.7532 (pm20) cc_final: 0.7077 (pm20) REVERT: G 277 MET cc_start: 0.8658 (ttp) cc_final: 0.8418 (ttt) REVERT: G 283 GLU cc_start: 0.7925 (pm20) cc_final: 0.7078 (pt0) REVERT: G 329 MET cc_start: 0.8450 (mmm) cc_final: 0.7737 (mmm) REVERT: G 438 LEU cc_start: 0.8974 (mt) cc_final: 0.8499 (tp) REVERT: G 605 GLN cc_start: 0.8459 (tt0) cc_final: 0.7970 (tt0) REVERT: G 652 ASN cc_start: 0.8893 (p0) cc_final: 0.8674 (p0) REVERT: G 707 MET cc_start: 0.9157 (mmt) cc_final: 0.8897 (mmp) REVERT: G 712 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8875 (tppt) REVERT: H 91 MET cc_start: 0.9145 (mpp) cc_final: 0.8871 (mpp) REVERT: H 92 PRO cc_start: 0.8818 (Cg_exo) cc_final: 0.8609 (Cg_endo) REVERT: H 143 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8328 (mt-10) REVERT: H 169 GLN cc_start: 0.8344 (mt0) cc_final: 0.7890 (mt0) REVERT: H 172 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7304 (tmm) REVERT: H 183 MET cc_start: 0.8612 (mtt) cc_final: 0.8339 (mtt) REVERT: H 184 MET cc_start: 0.9002 (mmm) cc_final: 0.8797 (mmm) REVERT: H 202 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8118 (tm-30) REVERT: H 206 GLU cc_start: 0.8148 (mp0) cc_final: 0.7691 (mp0) REVERT: H 228 TYR cc_start: 0.8765 (m-80) cc_final: 0.8543 (m-80) REVERT: H 261 MET cc_start: 0.8183 (mmm) cc_final: 0.7871 (mmt) REVERT: H 279 ARG cc_start: 0.7547 (ptm160) cc_final: 0.7104 (ptm160) REVERT: I 94 SER cc_start: 0.9497 (t) cc_final: 0.8879 (p) REVERT: I 200 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8044 (tm-30) REVERT: I 204 ASN cc_start: 0.8819 (m-40) cc_final: 0.8522 (t0) REVERT: I 206 GLN cc_start: 0.8269 (tp40) cc_final: 0.7980 (tp-100) REVERT: P 97 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7867 (pmm) REVERT: P 133 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7900 (tt0) REVERT: P 134 TRP cc_start: 0.8837 (p90) cc_final: 0.8416 (p90) REVERT: P 174 MET cc_start: 0.8559 (mmm) cc_final: 0.8303 (mmp) REVERT: P 181 LEU cc_start: 0.9373 (mt) cc_final: 0.9082 (mp) REVERT: P 296 PHE cc_start: 0.8733 (p90) cc_final: 0.8525 (p90) REVERT: P 298 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8531 (t80) REVERT: P 360 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8350 (tmt-80) REVERT: R 110 GLN cc_start: 0.7693 (mp10) cc_final: 0.7289 (mp10) REVERT: T 90 TYR cc_start: 0.6921 (t80) cc_final: 0.6140 (t80) REVERT: T 108 LEU cc_start: 0.5642 (mp) cc_final: 0.4797 (tt) REVERT: T 114 ASP cc_start: 0.9077 (m-30) cc_final: 0.8870 (m-30) REVERT: T 117 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8121 (tm-30) REVERT: T 143 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7506 (mp0) REVERT: T 147 TYR cc_start: 0.8092 (t80) cc_final: 0.7883 (t80) REVERT: V 85 GLU cc_start: 0.8637 (pp20) cc_final: 0.8147 (pt0) REVERT: W 45 GLU cc_start: 0.8974 (tp30) cc_final: 0.8151 (tp30) REVERT: W 68 GLU cc_start: 0.8709 (pt0) cc_final: 0.8425 (pp20) REVERT: W 118 PRO cc_start: 0.8254 (Cg_exo) cc_final: 0.7987 (Cg_endo) REVERT: W 124 LYS cc_start: 0.8773 (tptt) cc_final: 0.8042 (tptt) REVERT: W 126 TYR cc_start: 0.9236 (m-80) cc_final: 0.8844 (m-80) REVERT: X 26 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8828 (ttpt) REVERT: X 37 ASP cc_start: 0.6772 (p0) cc_final: 0.5879 (p0) REVERT: X 47 ARG cc_start: 0.8003 (tpt170) cc_final: 0.7072 (tpt90) REVERT: Z 80 ASP cc_start: 0.7974 (m-30) cc_final: 0.7410 (m-30) REVERT: Z 86 ILE cc_start: 0.8931 (mm) cc_final: 0.8673 (tt) REVERT: a 5 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9118 (mm) REVERT: a 48 MET cc_start: 0.8798 (mmm) cc_final: 0.8447 (mmm) REVERT: a 61 TYR cc_start: 0.7944 (t80) cc_final: 0.7370 (t80) REVERT: b 43 SER cc_start: 0.9093 (p) cc_final: 0.8843 (m) REVERT: b 47 LYS cc_start: 0.9239 (tptt) cc_final: 0.8650 (ttpp) REVERT: b 84 LEU cc_start: 0.9061 (tp) cc_final: 0.8849 (tt) REVERT: q 86 TRP cc_start: 0.8721 (m100) cc_final: 0.8026 (m100) outliers start: 138 outliers final: 112 residues processed: 949 average time/residue: 0.2103 time to fit residues: 332.0610 Evaluate side-chains 965 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 842 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 266 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 360 ARG Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 386 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 362 optimal weight: 0.9980 chunk 3 optimal weight: 0.0770 chunk 373 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 169 GLN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077355 restraints weight = 103816.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079892 restraints weight = 48827.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081559 restraints weight = 29499.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.082689 restraints weight = 21023.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083422 restraints weight = 16717.607| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 34709 Z= 0.154 Angle : 0.985 77.422 47099 Z= 0.382 Chirality : 0.046 0.258 5150 Planarity : 0.006 0.131 5975 Dihedral : 7.936 170.186 4792 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 3.49 % Allowed : 26.05 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4136 helix: 0.48 (0.12), residues: 1858 sheet: -1.25 (0.28), residues: 346 loop : -1.29 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG S 26 TYR 0.054 0.002 TYR E 112 PHE 0.032 0.002 PHE A 62 TRP 0.045 0.001 TRP b 80 HIS 0.009 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00367 (34668) covalent geometry : angle 0.76848 (47007) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.67103 ( 8) hydrogen bonds : bond 0.03948 ( 1355) hydrogen bonds : angle 5.13031 ( 3849) metal coordination : bond 0.01538 ( 37) metal coordination : angle 14.62617 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 866 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8356 (tpp80) cc_final: 0.6563 (ptt180) REVERT: A 82 ILE cc_start: 0.8691 (tp) cc_final: 0.8476 (tp) REVERT: A 98 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8587 (mm) REVERT: A 106 TRP cc_start: 0.7740 (t60) cc_final: 0.7511 (t60) REVERT: B 103 GLU cc_start: 0.8301 (tp30) cc_final: 0.8067 (tp30) REVERT: C 47 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7568 (tpt170) REVERT: C 106 GLN cc_start: 0.8487 (mp10) cc_final: 0.8098 (mp10) REVERT: C 108 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8689 (mmmt) REVERT: C 199 LYS cc_start: 0.9455 (tppt) cc_final: 0.8969 (tppp) REVERT: C 216 LYS cc_start: 0.9168 (tptt) cc_final: 0.8900 (mptt) REVERT: D 121 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7981 (mp0) REVERT: D 204 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8414 (m-10) REVERT: D 210 MET cc_start: 0.8615 (mtm) cc_final: 0.8289 (mpp) REVERT: D 214 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7355 (t80) REVERT: D 215 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8475 (tm-30) REVERT: D 443 MET cc_start: 0.7599 (mmt) cc_final: 0.7189 (mmt) REVERT: E 59 TYR cc_start: 0.8428 (m-80) cc_final: 0.8078 (m-80) REVERT: E 120 MET cc_start: 0.7123 (ttp) cc_final: 0.6721 (ttp) REVERT: E 122 ASN cc_start: 0.8178 (m-40) cc_final: 0.6457 (t0) REVERT: E 184 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7322 (ptt) REVERT: E 191 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: F 163 TYR cc_start: 0.7598 (t80) cc_final: 0.7309 (t80) REVERT: F 164 ASN cc_start: 0.7713 (p0) cc_final: 0.7223 (t0) REVERT: F 337 MET cc_start: 0.8475 (tpp) cc_final: 0.8246 (tpp) REVERT: F 349 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6639 (tp) REVERT: F 357 MET cc_start: 0.8120 (ttm) cc_final: 0.7403 (tmm) REVERT: G 42 MET cc_start: 0.6993 (tpp) cc_final: 0.6706 (tpp) REVERT: G 67 GLU cc_start: 0.8221 (tt0) cc_final: 0.7645 (tm-30) REVERT: G 117 MET cc_start: 0.8992 (mmm) cc_final: 0.8477 (mmm) REVERT: G 160 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8961 (t) REVERT: G 217 GLU cc_start: 0.7650 (pm20) cc_final: 0.7368 (pm20) REVERT: G 239 THR cc_start: 0.8961 (p) cc_final: 0.8734 (t) REVERT: G 271 MET cc_start: 0.8384 (mmm) cc_final: 0.8160 (mmm) REVERT: G 277 MET cc_start: 0.8595 (ttp) cc_final: 0.8386 (ttt) REVERT: G 283 GLU cc_start: 0.7867 (pm20) cc_final: 0.7010 (pt0) REVERT: G 329 MET cc_start: 0.8382 (mmm) cc_final: 0.7905 (mmm) REVERT: G 438 LEU cc_start: 0.9014 (mt) cc_final: 0.8585 (tp) REVERT: G 471 LYS cc_start: 0.9209 (ttmt) cc_final: 0.8999 (ttmm) REVERT: G 579 MET cc_start: 0.8753 (ptp) cc_final: 0.8464 (ptm) REVERT: G 605 GLN cc_start: 0.8451 (tt0) cc_final: 0.8009 (tt0) REVERT: G 652 ASN cc_start: 0.8815 (p0) cc_final: 0.8583 (p0) REVERT: G 712 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8895 (tppt) REVERT: H 91 MET cc_start: 0.9088 (mpp) cc_final: 0.8814 (mpp) REVERT: H 92 PRO cc_start: 0.8771 (Cg_exo) cc_final: 0.8562 (Cg_endo) REVERT: H 126 LYS cc_start: 0.7974 (ptpp) cc_final: 0.7533 (pttp) REVERT: H 172 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7203 (tmm) REVERT: H 183 MET cc_start: 0.8565 (mtt) cc_final: 0.8085 (mtp) REVERT: H 206 GLU cc_start: 0.8079 (mp0) cc_final: 0.7647 (mp0) REVERT: H 228 TYR cc_start: 0.8775 (m-80) cc_final: 0.8573 (m-80) REVERT: H 279 ARG cc_start: 0.7495 (ptm160) cc_final: 0.7012 (ptm160) REVERT: I 94 SER cc_start: 0.9503 (t) cc_final: 0.8881 (p) REVERT: I 204 ASN cc_start: 0.8780 (m-40) cc_final: 0.8492 (t0) REVERT: I 206 GLN cc_start: 0.8221 (tp40) cc_final: 0.7903 (tp-100) REVERT: P 97 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7892 (pmm) REVERT: P 133 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7955 (tt0) REVERT: P 134 TRP cc_start: 0.8821 (p90) cc_final: 0.8401 (p90) REVERT: P 174 MET cc_start: 0.8531 (mmm) cc_final: 0.8271 (mmp) REVERT: P 181 LEU cc_start: 0.9389 (mt) cc_final: 0.9083 (mp) REVERT: P 296 PHE cc_start: 0.8723 (p90) cc_final: 0.8522 (p90) REVERT: P 298 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8537 (t80) REVERT: P 360 ARG cc_start: 0.8964 (tpt90) cc_final: 0.8335 (tmt-80) REVERT: Q 108 GLU cc_start: 0.8219 (mp0) cc_final: 0.8004 (mp0) REVERT: R 110 GLN cc_start: 0.7621 (mp10) cc_final: 0.7253 (mp10) REVERT: T 82 ARG cc_start: 0.8525 (mmm160) cc_final: 0.8128 (mtp180) REVERT: T 85 TYR cc_start: 0.8273 (t80) cc_final: 0.7811 (t80) REVERT: T 90 TYR cc_start: 0.6816 (t80) cc_final: 0.6226 (t80) REVERT: T 104 PHE cc_start: 0.7711 (m-80) cc_final: 0.7511 (m-80) REVERT: T 108 LEU cc_start: 0.5702 (mp) cc_final: 0.4749 (tt) REVERT: T 115 GLN cc_start: 0.8769 (tt0) cc_final: 0.8211 (tm-30) REVERT: T 143 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7455 (mp0) REVERT: V 50 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: V 54 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8446 (pm20) REVERT: V 85 GLU cc_start: 0.8594 (pp20) cc_final: 0.8186 (pt0) REVERT: W 45 GLU cc_start: 0.8911 (tp30) cc_final: 0.8123 (tp30) REVERT: W 58 THR cc_start: 0.8101 (m) cc_final: 0.7588 (p) REVERT: W 68 GLU cc_start: 0.8609 (pt0) cc_final: 0.8345 (pp20) REVERT: W 124 LYS cc_start: 0.8757 (tptt) cc_final: 0.8043 (tptt) REVERT: W 126 TYR cc_start: 0.9215 (m-80) cc_final: 0.8870 (m-80) REVERT: X 26 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8830 (ttpt) REVERT: X 37 ASP cc_start: 0.6790 (p0) cc_final: 0.5954 (p0) REVERT: X 47 ARG cc_start: 0.8142 (tpt170) cc_final: 0.7151 (tpt90) REVERT: Z 86 ILE cc_start: 0.8919 (mm) cc_final: 0.8677 (tt) REVERT: Z 93 GLU cc_start: 0.8135 (tp30) cc_final: 0.7802 (tp30) REVERT: Z 133 MET cc_start: 0.7898 (tpt) cc_final: 0.7663 (tpt) REVERT: a 5 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9087 (mm) REVERT: a 48 MET cc_start: 0.8738 (mmm) cc_final: 0.8381 (mmm) REVERT: a 61 TYR cc_start: 0.7887 (t80) cc_final: 0.7332 (t80) REVERT: b 43 SER cc_start: 0.9061 (p) cc_final: 0.8799 (m) REVERT: b 47 LYS cc_start: 0.9201 (tptt) cc_final: 0.8610 (ttpp) REVERT: q 86 TRP cc_start: 0.8779 (m100) cc_final: 0.8220 (m100) outliers start: 127 outliers final: 101 residues processed: 934 average time/residue: 0.2135 time to fit residues: 331.8349 Evaluate side-chains 956 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 841 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 266 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 54 GLU Chi-restraints excluded: chain W residue 33 ARG Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 402 optimal weight: 0.0770 chunk 34 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 378 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 361 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 379 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 382 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN F 376 HIS ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075478 restraints weight = 103505.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077953 restraints weight = 49053.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079581 restraints weight = 29819.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.080682 restraints weight = 21346.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081413 restraints weight = 17012.116| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34709 Z= 0.195 Angle : 1.018 79.307 47099 Z= 0.394 Chirality : 0.047 0.244 5150 Planarity : 0.006 0.131 5975 Dihedral : 7.989 173.045 4792 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 3.49 % Allowed : 26.27 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 4136 helix: 0.44 (0.12), residues: 1866 sheet: -1.24 (0.28), residues: 345 loop : -1.31 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 82 TYR 0.053 0.002 TYR E 112 PHE 0.040 0.002 PHE A 62 TRP 0.037 0.002 TRP b 80 HIS 0.010 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00460 (34668) covalent geometry : angle 0.78592 (47007) SS BOND : bond 0.00212 ( 4) SS BOND : angle 0.61805 ( 8) hydrogen bonds : bond 0.04059 ( 1355) hydrogen bonds : angle 5.20515 ( 3849) metal coordination : bond 0.01971 ( 37) metal coordination : angle 15.32672 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8278.95 seconds wall clock time: 143 minutes 29.27 seconds (8609.27 seconds total)