Starting phenix.real_space_refine on Wed May 6 00:02:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnl_38506/05_2026/8xnl_38506_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnl_38506/05_2026/8xnl_38506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnl_38506/05_2026/8xnl_38506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnl_38506/05_2026/8xnl_38506.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnl_38506/05_2026/8xnl_38506_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnl_38506/05_2026/8xnl_38506_neut.cif" } resolution = 3.1 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= 0.002 sd= 0.104 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 13 5.49 5 S 246 5.16 5 C 22113 2.51 5 N 5872 2.21 5 O 6270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.04s 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: 34543 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 754 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 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: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} 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: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2517 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 22, 'TRANS': 292} Chain breaks: 2 Chain: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} 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: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} 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: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} 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: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 11, 'TRANS': 67} Chain: "q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1192 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "r" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "s" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 189 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} 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: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'3PE': 1, 'PC1': 1, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "q" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1017 SG CYS B 99 82.947 58.284 105.371 1.00 29.52 S ATOM 1750 SG CYS B 194 85.867 55.139 109.012 1.00 29.28 S ATOM 1023 SG CYS B 100 81.241 53.903 104.136 1.00 30.11 S ATOM 1520 SG CYS B 164 80.261 54.718 110.166 1.00 28.96 S ATOM 7530 SG CYS E 134 143.248 50.507 151.007 1.00 56.01 S ATOM 7564 SG CYS E 139 146.221 52.039 150.015 1.00 56.50 S ATOM 7848 SG CYS E 175 141.179 54.209 153.449 1.00 54.42 S ATOM 7871 SG CYS E 179 144.070 55.917 154.189 1.00 57.95 S ATOM 11401 SG CYS F 425 124.708 60.027 153.668 1.00 45.60 S ATOM 11079 SG CYS F 385 124.652 57.443 147.923 1.00 39.95 S ATOM 11059 SG CYS F 382 120.423 58.653 150.236 1.00 40.29 S ATOM 11040 SG CYS F 379 122.427 54.639 153.143 1.00 43.09 S ATOM 12449 SG CYS G 131 104.183 47.182 137.279 1.00 31.31 S ATOM 12428 SG CYS G 128 106.125 50.902 132.555 1.00 30.26 S ATOM 12489 SG CYS G 137 103.867 53.121 138.553 1.00 33.13 S ATOM 13174 SG CYS G 226 105.836 47.411 145.841 1.00 34.31 S ATOM 12845 SG CYS G 182 109.064 45.887 151.590 1.00 36.31 S ATOM 12821 SG CYS G 179 108.404 51.399 148.915 1.00 35.62 S ATOM 12798 SG CYS G 176 111.815 47.070 146.508 1.00 34.05 S ATOM 11935 SG CYS G 64 109.836 57.489 150.753 1.00 35.53 S ATOM 12021 SG CYS G 75 110.538 59.488 149.025 1.00 36.47 S ATOM 12046 SG CYS G 78 109.657 63.758 150.859 1.00 36.76 S ATOM 12147 SG CYS G 92 108.884 61.814 154.133 1.00 39.04 S ATOM 20187 SG CYS I 123 89.590 49.925 118.620 1.00 27.30 S ATOM 20413 SG CYS I 152 89.238 48.627 113.546 1.00 27.39 S ATOM 20460 SG CYS I 158 94.938 48.797 115.541 1.00 26.60 S ATOM 20439 SG CYS I 155 91.861 53.231 115.163 1.00 27.04 S ATOM 20136 SG CYS I 116 99.542 45.993 125.923 1.00 29.24 S ATOM 20159 SG CYS I 119 95.109 45.613 122.660 1.00 28.85 S ATOM 20117 SG CYS I 113 98.293 40.781 122.816 1.00 28.61 S ATOM 20489 SG CYS I 162 101.181 45.305 120.540 1.00 28.07 S ATOM 24988 SG CYS R 79 114.669 38.787 124.633 1.00 32.60 S ATOM 25164 SG CYS R 104 111.989 39.327 127.225 1.00 32.49 S ATOM 25186 SG CYS R 107 111.713 38.005 123.092 1.00 30.78 S Time building chain proxies: 7.50, per 1000 atoms: 0.22 Number of scatterers: 34543 At special positions: 0 Unit cell: (171.6, 126.5, 202.4, 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 13 15.00 O 6270 8.00 N 5872 7.00 C 22113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.02 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 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: 3.53 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 175 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " 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 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 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="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="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE1 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=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " Number of angles added : 3 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7966 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 33 sheets defined 49.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 52 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 removed outlier: 3.637A pdb=" N ASP B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 4.014A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.710A pdb=" N LYS B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) 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: 4.013A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 58 " --> pdb=" O HIS C 54 " (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 161 through 174 removed outlier: 4.116A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (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: 3.856A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.298A 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: 3.827A 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: 4.174A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.563A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.891A 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: 3.660A 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: 3.702A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.207A 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: 3.738A 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: 3.670A 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: 3.531A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.256A 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: 3.952A 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 removed outlier: 3.680A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 143 through 156 removed outlier: 4.163A pdb=" N ILE E 147 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.577A pdb=" N ILE E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 201 " --> pdb=" O PRO E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 101 Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.554A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.923A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.515A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.831A 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 266 removed outlier: 3.602A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.533A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.562A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 335 removed outlier: 4.186A pdb=" N THR F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.548A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.661A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.775A 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: 4.350A 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: 3.598A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.725A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.714A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 147 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.933A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.818A 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 360 Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.670A 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: 4.026A 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: 4.007A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.638A 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 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 629 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.522A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) 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: 4.301A 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: 3.749A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.533A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 85 removed outlier: 3.551A pdb=" N PHE H 71 " --> pdb=" O SER H 67 " (cutoff:3.500A) Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 100 through 123 removed outlier: 3.688A 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: 4.551A 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: 3.568A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.520A pdb=" N ALA H 135 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 3.798A 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: 3.736A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.539A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) 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 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.528A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.867A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.143A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.804A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.669A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.194A 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 112 through 122 removed outlier: 4.106A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.598A 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 removed outlier: 3.625A pdb=" N ALA P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.754A pdb=" N ARG P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 219 removed outlier: 4.081A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 222 No H-bonds generated for 'chain 'P' and resid 220 through 222' Processing helix chain 'P' and resid 229 through 232 Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 272 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.882A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER P 308 " --> pdb=" O LEU P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.033A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 358 through 363 removed outlier: 4.675A pdb=" N SER P 363 " --> pdb=" O TYR P 359 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.414A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 165 Processing helix chain 'R' and resid 44 through 49 removed outlier: 3.727A pdb=" N PHE R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 67 removed outlier: 4.039A pdb=" N ALA R 65 " --> pdb=" O ILE R 61 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 5.952A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (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 126 Processing helix chain 'T' and resid 131 through 138 removed outlier: 3.678A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.678A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.587A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 removed outlier: 3.616A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 98 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 128 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.510A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.426A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA X 34 " --> pdb=" O HIS X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 52 through 77 removed outlier: 3.574A pdb=" N CYS X 56 " --> pdb=" O ASP X 52 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS X 58 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU X 59 " --> pdb=" O ARG X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.945A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 111 Processing helix chain 'X' and resid 140 through 144 removed outlier: 3.992A pdb=" N SER X 144 " --> pdb=" O PRO X 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 99 removed outlier: 3.534A pdb=" N GLY Z 39 " --> pdb=" O MET Z 35 " (cutoff:3.500A) Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 1 through 3 No H-bonds generated for 'chain 'a' and resid 1 through 3' Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.633A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.599A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR a 30 " --> pdb=" O ILE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.760A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.556A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 55 through 58 Processing helix chain 'q' and resid 78 through 82 Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.126A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 17 Processing helix chain 'r' and resid 53 through 57 Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.954A pdb=" N GLU r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL r 63 " --> pdb=" O GLY r 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 58 through 63' Processing helix chain 's' and resid 43 through 54 removed outlier: 4.202A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 96 removed outlier: 5.933A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.505A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.890A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.147A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.563A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.717A pdb=" N MET D 80 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 101 " --> pdb=" O MET D 80 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'D' and resid 397 through 401 removed outlier: 3.501A pdb=" N PHE D 407 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 171 through 173 removed outlier: 5.588A pdb=" N MET E 184 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 194 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 286 through 291 removed outlier: 3.514A pdb=" N GLU F 290 " --> pdb=" O LYS F 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.548A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 32 through 34 Processing sheet with id=AB5, first strand: chain 'G' and resid 79 through 80 Processing sheet with id=AB6, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.312A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.638A 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 308 Processing sheet with id=AB9, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.455A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA G 339 " --> pdb=" O PHE G 546 " (cutoff:3.500A) removed outlier: 6.703A 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: 6.203A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (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 100 through 103 Processing sheet with id=AC4, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.407A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.360A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC7, first strand: chain 'P' and resid 226 through 227 removed outlier: 6.120A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AC9, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD1, first strand: chain 'R' and resid 70 through 71 removed outlier: 5.820A pdb=" N ASN R 70 " --> pdb=" O LYS R 112 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 76 through 79 removed outlier: 3.588A pdb=" N VAL R 91 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 53 through 58 removed outlier: 3.576A pdb=" N LYS S 64 " --> pdb=" O HIS S 22 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD5, first strand: chain 'q' and resid 37 through 41 removed outlier: 6.594A pdb=" N TYR q 48 " --> pdb=" O VAL q 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'q' and resid 67 through 68 1451 hydrogen bonds defined for protein. 4182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.10 Time building geometry restraints manager: 4.46 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: 11606 1.37 - 1.58: 23291 1.58 - 1.80: 231 1.80 - 2.01: 165 2.01 - 2.23: 80 Bond restraints: 35373 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.648 0.730 2.00e-02 2.50e+03 1.33e+03 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 1.09e+02 bond pdb=" CA7 CDL q 201 " pdb=" OA8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.449 -0.115 1.10e-02 8.26e+03 1.09e+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 1.09e+02 bond pdb=" CA GLY F 234 " pdb=" C GLY F 234 " ideal model delta sigma weight residual 1.521 1.404 0.117 1.13e-02 7.83e+03 1.08e+02 ... (remaining 35368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.17: 47108 6.17 - 12.33: 624 12.33 - 18.50: 185 18.50 - 24.67: 7 24.67 - 30.84: 3 Bond angle restraints: 47927 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 114.39 89.00 25.39 1.45e+00 4.76e-01 3.07e+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 87.60 16.73 1.14e+00 7.69e-01 2.15e+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 87.46 16.87 1.20e+00 6.94e-01 1.98e+02 angle pdb=" N ILE G 632 " pdb=" CA ILE G 632 " pdb=" C ILE G 632 " ideal model delta sigma weight residual 107.80 88.00 19.80 1.45e+00 4.76e-01 1.86e+02 angle pdb=" N ILE G 251 " pdb=" CA ILE G 251 " pdb=" C ILE G 251 " ideal model delta sigma weight residual 108.17 126.79 -18.62 1.40e+00 5.10e-01 1.77e+02 ... (remaining 47922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.37: 20751 28.37 - 56.75: 558 56.75 - 85.12: 72 85.12 - 113.49: 6 113.49 - 141.87: 6 Dihedral angle restraints: 21393 sinusoidal: 9038 harmonic: 12355 Sorted by residual: dihedral pdb=" C ASP D 140 " pdb=" N ASP D 140 " pdb=" CA ASP D 140 " pdb=" CB ASP D 140 " ideal model delta harmonic sigma weight residual -122.60 -101.19 -21.41 0 2.50e+00 1.60e-01 7.34e+01 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 93.00 161.56 -68.56 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" C LEU G 387 " pdb=" N LEU G 387 " pdb=" CA LEU G 387 " pdb=" CB LEU G 387 " ideal model delta harmonic sigma weight residual -122.60 -105.64 -16.96 0 2.50e+00 1.60e-01 4.60e+01 ... (remaining 21390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 4708 0.181 - 0.362: 454 0.362 - 0.543: 38 0.543 - 0.724: 5 0.724 - 0.905: 24 Chirality restraints: 5229 Sorted by residual: chirality pdb="FE3 SF4 I 303 " pdb=" S1 SF4 I 303 " pdb=" S2 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False -10.55 -9.65 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb="FE4 SF4 G 802 " pdb=" S1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb="FE4 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 5226 not shown) Planarity restraints: 6085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 401 " -0.056 2.00e-02 2.50e+03 2.00e-01 1.20e+03 pdb=" C1M UQ9 H 401 " -0.343 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 401 " 0.138 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 401 " -0.038 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 401 " -0.047 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 401 " 0.085 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 401 " 0.012 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " -0.043 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 401 " 0.430 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 401 " -0.209 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 401 " -0.184 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 401 " 0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ9 H 401 " -0.117 2.00e-02 2.50e+03 9.87e-02 1.22e+02 pdb=" C13 UQ9 H 401 " 0.161 2.00e-02 2.50e+03 pdb=" C14 UQ9 H 401 " 0.034 2.00e-02 2.50e+03 pdb=" C15 UQ9 H 401 " 0.011 2.00e-02 2.50e+03 pdb=" C16 UQ9 H 401 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 H 401 " 0.075 2.00e-02 2.50e+03 7.47e-02 6.97e+01 pdb=" C11 UQ9 H 401 " -0.009 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " 0.089 2.00e-02 2.50e+03 pdb=" C8 UQ9 H 401 " -0.111 2.00e-02 2.50e+03 pdb=" C9 UQ9 H 401 " -0.044 2.00e-02 2.50e+03 ... (remaining 6082 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 76 2.38 - 3.01: 23943 3.01 - 3.64: 54443 3.64 - 4.27: 86638 4.27 - 4.90: 139670 Nonbonded interactions: 304770 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.756 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.970 3.040 nonbonded pdb=" O ASN H 97 " pdb=" OD1 ASN H 97 " model vdw 1.983 3.040 nonbonded pdb=" O PHE G 63 " pdb=" SG CYS G 64 " model vdw 2.009 3.400 nonbonded pdb=" N THR G 174 " pdb=" N ARG G 175 " model vdw 2.080 2.560 ... (remaining 304765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 40.770 Find NCS groups from input model: 0.240 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.022 1.049 35413 Z= 1.011 Angle : 2.170 48.474 48017 Z= 1.435 Chirality : 0.123 0.905 5229 Planarity : 0.008 0.200 6085 Dihedral : 13.022 141.868 13418 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 43.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 0.35 % Allowed : 7.47 % Favored : 92.18 % Cbeta Deviations : 1.36 % 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: -2.15 (0.12), residues: 4205 helix: -0.80 (0.11), residues: 1807 sheet: -1.21 (0.27), residues: 364 loop : -2.04 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 333 TYR 0.031 0.002 TYR D 311 PHE 0.029 0.002 PHE D 200 TRP 0.031 0.002 TRP V 114 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.01422 (35373) covalent geometry : angle 2.04615 (47927) SS BOND : bond 0.00962 ( 3) SS BOND : angle 2.44790 ( 6) hydrogen bonds : bond 0.23431 ( 1451) hydrogen bonds : angle 9.09651 ( 4182) metal coordination : bond 0.49977 ( 37) metal coordination : angle 17.37335 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1533 time to evaluate : 1.352 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: B 141 MET cc_start: 0.8035 (tpt) cc_final: 0.7803 (tpt) REVERT: B 160 SER cc_start: 0.8614 (t) cc_final: 0.8382 (m) REVERT: E 173 VAL cc_start: 0.8164 (p) cc_final: 0.7909 (m) REVERT: E 192 TYR cc_start: 0.7039 (m-80) cc_final: 0.6832 (m-80) REVERT: F 233 VAL cc_start: 0.8157 (t) cc_final: 0.7873 (p) REVERT: F 337 MET cc_start: 0.7479 (mmp) cc_final: 0.7232 (mmt) REVERT: G 660 GLU cc_start: 0.6385 (mm-30) cc_final: 0.5207 (tp30) REVERT: H 43 TYR cc_start: 0.8562 (m-80) cc_final: 0.8315 (m-80) REVERT: I 40 ASN cc_start: 0.8391 (t0) cc_final: 0.7791 (t0) REVERT: I 177 THR cc_start: 0.8434 (p) cc_final: 0.8193 (p) REVERT: P 355 ARG cc_start: 0.7346 (ptp-170) cc_final: 0.7089 (ttt180) REVERT: S 27 SER cc_start: 0.6848 (t) cc_final: 0.6570 (p) REVERT: S 64 LYS cc_start: 0.8577 (mtpp) cc_final: 0.7972 (mtmt) REVERT: Z 8 GLN cc_start: 0.7706 (tt0) cc_final: 0.7401 (tt0) outliers start: 13 outliers final: 2 residues processed: 1540 average time/residue: 0.2518 time to fit residues: 605.6558 Evaluate side-chains 905 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 903 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain S residue 68 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN B 172 HIS B 209 GLN C 56 GLN C 73 GLN C 88 HIS C 123 ASN C 180 HIS C 195 HIS D 88 HIS D 117 HIS D 131 GLN D 147 ASN D 168 GLN D 182 ASN D 190 HIS D 234 GLN D 346 GLN D 349 ASN D 381 HIS D 442 HIS E 73 HIS E 74 GLN E 188 ASN E 245 GLN F 44 ASN F 103 ASN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 220 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 ASN F 376 HIS F 393 ASN F 422 HIS F 455 GLN G 74 ASN G 123 ASN G 140 GLN G 142 GLN G 164 ASN ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN G 444 HIS G 460 HIS G 495 ASN G 571 HIS G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 705 GLN H 32 GLN H 47 GLN ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS H 258 ASN H 287 HIS P 71 ASN P 102 GLN P 171 ASN P 251 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 356 HIS Q 51 GLN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 HIS V 41 HIS W 73 ASN W 94 GLN W 105 HIS ** X 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 HIS Z 24 ASN Z 54 ASN Z 90 ASN a 27 HIS b 11 ASN b 62 ASN b 83 ASN ** q 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 GLN r 36 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 41 ASN s 49 ASN s 59 GLN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.120182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098279 restraints weight = 65136.577| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.22 r_work: 0.3215 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 35413 Z= 0.206 Angle : 0.950 52.989 48017 Z= 0.412 Chirality : 0.048 0.245 5229 Planarity : 0.007 0.139 6085 Dihedral : 10.224 158.005 5024 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 3.65 % Allowed : 15.30 % Favored : 81.05 % 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: -0.90 (0.12), residues: 4205 helix: 0.29 (0.12), residues: 1876 sheet: -1.04 (0.25), residues: 388 loop : -1.35 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 47 TYR 0.026 0.002 TYR T 90 PHE 0.028 0.002 PHE H 310 TRP 0.021 0.002 TRP V 114 HIS 0.009 0.001 HIS r 47 Details of bonding type rmsd covalent geometry : bond 0.00472 (35373) covalent geometry : angle 0.79312 (47927) SS BOND : bond 0.00154 ( 3) SS BOND : angle 1.30357 ( 6) hydrogen bonds : bond 0.05687 ( 1451) hydrogen bonds : angle 5.89382 ( 4182) metal coordination : bond 0.02741 ( 37) metal coordination : angle 12.51851 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 972 time to evaluate : 1.317 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 105 GLU cc_start: 0.9035 (tp30) cc_final: 0.8758 (tp30) REVERT: B 138 THR cc_start: 0.9001 (p) cc_final: 0.8800 (m) REVERT: C 216 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8824 (mmtm) REVERT: D 83 ASN cc_start: 0.8408 (t0) cc_final: 0.8186 (t0) REVERT: D 210 MET cc_start: 0.9044 (mtm) cc_final: 0.8612 (mtm) REVERT: D 270 ASN cc_start: 0.8634 (m-40) cc_final: 0.8396 (t0) REVERT: D 443 MET cc_start: 0.8299 (mpp) cc_final: 0.7651 (mpp) REVERT: E 59 TYR cc_start: 0.8698 (m-80) cc_final: 0.8368 (m-80) REVERT: E 143 ASP cc_start: 0.8694 (t0) cc_final: 0.8241 (t0) REVERT: E 191 TYR cc_start: 0.8063 (m-80) cc_final: 0.7863 (m-80) REVERT: F 233 VAL cc_start: 0.8277 (t) cc_final: 0.7838 (p) REVERT: G 32 ILE cc_start: 0.8991 (mm) cc_final: 0.8746 (mt) REVERT: G 42 MET cc_start: 0.8949 (mtp) cc_final: 0.8694 (tpp) REVERT: G 44 GLU cc_start: 0.8000 (mp0) cc_final: 0.7795 (tt0) REVERT: G 117 MET cc_start: 0.8816 (mmt) cc_final: 0.8480 (mmt) REVERT: G 467 LYS cc_start: 0.7839 (mmtm) cc_final: 0.7605 (mmtp) REVERT: G 569 GLN cc_start: 0.7760 (tt0) cc_final: 0.7430 (tt0) REVERT: G 698 ASP cc_start: 0.7998 (p0) cc_final: 0.7787 (p0) REVERT: H 17 MET cc_start: 0.9179 (tmm) cc_final: 0.8859 (tmm) REVERT: H 43 TYR cc_start: 0.9156 (m-80) cc_final: 0.8529 (m-80) REVERT: H 224 PHE cc_start: 0.8425 (t80) cc_final: 0.7939 (t80) REVERT: P 174 MET cc_start: 0.8448 (tpt) cc_final: 0.8224 (tpt) REVERT: P 200 ILE cc_start: 0.8365 (mt) cc_final: 0.8030 (pt) REVERT: P 355 ARG cc_start: 0.8319 (ptp-170) cc_final: 0.6981 (ttt180) REVERT: R 71 GLU cc_start: 0.8111 (tt0) cc_final: 0.7535 (tm-30) REVERT: R 73 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6666 (mm-30) REVERT: R 80 ASP cc_start: 0.8879 (p0) cc_final: 0.8601 (p0) REVERT: S 64 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8057 (mtmt) REVERT: T 125 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7440 (tm-30) REVERT: T 126 PHE cc_start: 0.8523 (m-80) cc_final: 0.8284 (m-10) REVERT: T 147 TYR cc_start: 0.8706 (t80) cc_final: 0.8425 (t80) REVERT: V 33 ASP cc_start: 0.8999 (t0) cc_final: 0.8539 (m-30) REVERT: W 19 SER cc_start: 0.7943 (m) cc_final: 0.7674 (p) REVERT: X 46 CYS cc_start: 0.8533 (m) cc_final: 0.8016 (t) REVERT: X 93 ASN cc_start: 0.8525 (p0) cc_final: 0.8241 (p0) REVERT: Z 76 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8473 (tp40) REVERT: Z 98 MET cc_start: 0.6188 (mmp) cc_final: 0.5799 (mmp) REVERT: a 36 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8548 (ttpp) REVERT: a 48 MET cc_start: 0.8696 (mtp) cc_final: 0.8390 (mtp) REVERT: b 41 TYR cc_start: 0.8696 (m-10) cc_final: 0.8494 (m-10) REVERT: b 44 MET cc_start: 0.8564 (mtp) cc_final: 0.8261 (mtt) REVERT: b 45 ILE cc_start: 0.9200 (tt) cc_final: 0.8899 (pt) REVERT: q 95 ASP cc_start: 0.8418 (p0) cc_final: 0.8080 (p0) REVERT: q 96 ASP cc_start: 0.8680 (m-30) cc_final: 0.8399 (m-30) REVERT: r 57 ARG cc_start: 0.6843 (ptt90) cc_final: 0.6528 (ptt-90) REVERT: s 47 ASP cc_start: 0.7657 (m-30) cc_final: 0.7390 (m-30) REVERT: s 53 SER cc_start: 0.8347 (t) cc_final: 0.8103 (p) outliers start: 135 outliers final: 62 residues processed: 1044 average time/residue: 0.2237 time to fit residues: 380.0867 Evaluate side-chains 854 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 791 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 GLU Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 108 ASP Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 99 LYS Chi-restraints excluded: chain Z residue 112 HIS Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 71 GLN Chi-restraints excluded: chain q residue 24 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 5 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 399 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 275 optimal weight: 20.0000 chunk 245 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 335 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 127 GLN C 74 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 HIS F 455 GLN F 457 HIS G 140 GLN ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 522 GLN G 569 GLN ** G 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 705 GLN H 99 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 GLN Q 163 ASN ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN X 40 ASN X 69 ASN X 99 HIS Z 24 ASN Z 55 GLN ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 62 ASN b 83 ASN q 87 HIS q 91 HIS q 101 ASN q 123 GLN r 18 GLN r 29 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.093645 restraints weight = 65606.088| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.23 r_work: 0.3139 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 35413 Z= 0.198 Angle : 0.881 56.827 48017 Z= 0.358 Chirality : 0.046 0.188 5229 Planarity : 0.006 0.137 6085 Dihedral : 9.942 160.249 5020 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 4.03 % Allowed : 16.81 % Favored : 79.16 % 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: -0.44 (0.13), residues: 4205 helix: 0.68 (0.12), residues: 1882 sheet: -1.07 (0.25), residues: 384 loop : -1.06 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 111 TYR 0.027 0.002 TYR W 43 PHE 0.026 0.002 PHE F 162 TRP 0.023 0.002 TRP E 91 HIS 0.008 0.001 HIS F 303 Details of bonding type rmsd covalent geometry : bond 0.00465 (35373) covalent geometry : angle 0.69839 (47927) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.87793 ( 6) hydrogen bonds : bond 0.04783 ( 1451) hydrogen bonds : angle 5.47438 ( 4182) metal coordination : bond 0.02802 ( 37) metal coordination : angle 12.86831 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 844 time to evaluate : 1.424 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: C 104 ASN cc_start: 0.8562 (m110) cc_final: 0.8336 (m110) REVERT: C 112 ASP cc_start: 0.8502 (t0) cc_final: 0.8257 (t70) REVERT: D 108 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8657 (ttpt) REVERT: D 270 ASN cc_start: 0.8697 (m-40) cc_final: 0.8421 (t0) REVERT: D 389 TYR cc_start: 0.8315 (m-10) cc_final: 0.8099 (m-10) REVERT: E 143 ASP cc_start: 0.8788 (t0) cc_final: 0.8305 (t0) REVERT: E 165 ASP cc_start: 0.8712 (p0) cc_final: 0.8377 (p0) REVERT: E 191 TYR cc_start: 0.8502 (m-80) cc_final: 0.8258 (m-80) REVERT: E 194 ASP cc_start: 0.8328 (t70) cc_final: 0.8051 (t70) REVERT: F 131 MET cc_start: 0.8858 (mtm) cc_final: 0.8610 (mtt) REVERT: G 244 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8306 (mt-10) REVERT: G 467 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7632 (mmtp) REVERT: H 15 ILE cc_start: 0.9105 (mm) cc_final: 0.8836 (mt) REVERT: H 68 MET cc_start: 0.8215 (tpt) cc_final: 0.7992 (tpp) REVERT: H 224 PHE cc_start: 0.8496 (t80) cc_final: 0.7828 (t80) REVERT: H 264 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8845 (mt) REVERT: I 40 ASN cc_start: 0.9283 (t0) cc_final: 0.8879 (t0) REVERT: I 76 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7379 (t80) REVERT: I 165 ASP cc_start: 0.8770 (t0) cc_final: 0.8512 (t0) REVERT: I 208 ASP cc_start: 0.8592 (t70) cc_final: 0.7891 (t70) REVERT: P 279 TYR cc_start: 0.8228 (t80) cc_final: 0.7995 (t80) REVERT: P 324 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8128 (mm) REVERT: P 355 ARG cc_start: 0.8329 (ptp-170) cc_final: 0.7023 (ttt180) REVERT: Q 159 SER cc_start: 0.8367 (p) cc_final: 0.8166 (t) REVERT: R 45 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7701 (mtm180) REVERT: S 62 GLN cc_start: 0.8854 (mt0) cc_final: 0.8586 (mt0) REVERT: S 64 LYS cc_start: 0.9164 (mtpp) cc_final: 0.8165 (mtmt) REVERT: T 80 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8420 (tptt) REVERT: T 104 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7042 (p90) REVERT: T 125 GLU cc_start: 0.8562 (tm-30) cc_final: 0.7656 (tm-30) REVERT: T 126 PHE cc_start: 0.8783 (m-80) cc_final: 0.8582 (m-10) REVERT: T 142 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7949 (tp-100) REVERT: T 147 TYR cc_start: 0.8604 (t80) cc_final: 0.8321 (t80) REVERT: V 33 ASP cc_start: 0.9000 (t0) cc_final: 0.8547 (m-30) REVERT: W 98 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8147 (ttmm) REVERT: X 36 CYS cc_start: 0.8915 (m) cc_final: 0.8335 (m) REVERT: X 44 MET cc_start: 0.8196 (tpp) cc_final: 0.7081 (mmm) REVERT: X 46 CYS cc_start: 0.8701 (m) cc_final: 0.8178 (t) REVERT: X 52 ASP cc_start: 0.8247 (t0) cc_final: 0.7849 (t0) REVERT: X 55 ARG cc_start: 0.8525 (mmm160) cc_final: 0.7980 (mmt180) REVERT: X 93 ASN cc_start: 0.8539 (p0) cc_final: 0.8261 (p0) REVERT: X 108 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: Z 24 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7231 (t0) REVERT: Z 76 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8439 (tp-100) REVERT: b 45 ILE cc_start: 0.9097 (tt) cc_final: 0.8860 (pt) REVERT: q 47 LYS cc_start: 0.8720 (mttp) cc_final: 0.8501 (mttp) REVERT: q 53 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8332 (ptpp) REVERT: r 6 ARG cc_start: 0.8586 (mmm160) cc_final: 0.8037 (mmm160) REVERT: r 40 LYS cc_start: 0.8904 (tttm) cc_final: 0.8676 (tptm) REVERT: s 48 LEU cc_start: 0.8722 (mt) cc_final: 0.8514 (mp) outliers start: 149 outliers final: 81 residues processed: 933 average time/residue: 0.2177 time to fit residues: 331.8068 Evaluate side-chains 838 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 751 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 79 ILE Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 24 PHE Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 108 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 24 ASN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 71 GLN Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 107 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 82 optimal weight: 0.0000 chunk 29 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 242 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 152 GLN E 188 ASN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 HIS ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 569 GLN ** G 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 269 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 GLN V 50 GLN ** X 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 HIS b 62 ASN q 12 GLN q 101 ASN q 123 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.115418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093211 restraints weight = 65207.849| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.15 r_work: 0.3155 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35413 Z= 0.150 Angle : 0.825 58.429 48017 Z= 0.331 Chirality : 0.043 0.182 5229 Planarity : 0.005 0.131 6085 Dihedral : 9.711 162.242 5020 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 3.84 % Allowed : 17.62 % Favored : 78.53 % 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: -0.27 (0.13), residues: 4205 helix: 0.84 (0.12), residues: 1875 sheet: -1.05 (0.26), residues: 382 loop : -0.97 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 52 TYR 0.024 0.002 TYR W 43 PHE 0.025 0.002 PHE X 70 TRP 0.031 0.001 TRP E 91 HIS 0.007 0.001 HIS F 303 Details of bonding type rmsd covalent geometry : bond 0.00350 (35373) covalent geometry : angle 0.65084 (47927) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.73737 ( 6) hydrogen bonds : bond 0.04285 ( 1451) hydrogen bonds : angle 5.25472 ( 4182) metal coordination : bond 0.01930 ( 37) metal coordination : angle 12.14297 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 822 time to evaluate : 1.414 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: A 87 MET cc_start: 0.8902 (tmm) cc_final: 0.8502 (tmm) REVERT: D 108 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8645 (ttpt) REVERT: D 208 GLU cc_start: 0.8498 (tp30) cc_final: 0.8010 (tm-30) REVERT: D 270 ASN cc_start: 0.8674 (m-40) cc_final: 0.8402 (t0) REVERT: D 389 TYR cc_start: 0.8250 (m-10) cc_final: 0.8009 (m-10) REVERT: E 143 ASP cc_start: 0.8693 (t0) cc_final: 0.8217 (t0) REVERT: E 165 ASP cc_start: 0.8695 (p0) cc_final: 0.8409 (p0) REVERT: E 188 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7458 (m-40) REVERT: E 191 TYR cc_start: 0.8611 (m-80) cc_final: 0.8392 (m-80) REVERT: E 194 ASP cc_start: 0.8341 (t70) cc_final: 0.8079 (t70) REVERT: F 63 TYR cc_start: 0.8145 (t80) cc_final: 0.7891 (t80) REVERT: F 80 MET cc_start: 0.8972 (mmm) cc_final: 0.8715 (mmm) REVERT: F 131 MET cc_start: 0.8776 (mtm) cc_final: 0.8530 (mtt) REVERT: F 214 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8019 (mt-10) REVERT: F 292 MET cc_start: 0.8595 (ttm) cc_final: 0.8100 (mtp) REVERT: G 32 ILE cc_start: 0.9080 (mt) cc_final: 0.8708 (tt) REVERT: G 244 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8178 (mt-10) REVERT: G 467 LYS cc_start: 0.7883 (mmtm) cc_final: 0.7667 (mmtp) REVERT: H 15 ILE cc_start: 0.9107 (mm) cc_final: 0.8874 (mt) REVERT: H 68 MET cc_start: 0.8262 (tpt) cc_final: 0.7966 (tpp) REVERT: H 224 PHE cc_start: 0.8377 (t80) cc_final: 0.7974 (t80) REVERT: I 40 ASN cc_start: 0.9160 (t0) cc_final: 0.8872 (t0) REVERT: I 76 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7344 (t80) REVERT: I 165 ASP cc_start: 0.8742 (t0) cc_final: 0.8385 (t0) REVERT: I 208 ASP cc_start: 0.8578 (t70) cc_final: 0.8028 (t70) REVERT: P 78 SER cc_start: 0.9035 (m) cc_final: 0.8754 (p) REVERT: P 147 ASN cc_start: 0.8438 (t0) cc_final: 0.8136 (m-40) REVERT: P 336 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: P 355 ARG cc_start: 0.8348 (ptp-170) cc_final: 0.7023 (ttt180) REVERT: Q 55 VAL cc_start: 0.7601 (m) cc_final: 0.7339 (p) REVERT: R 45 ARG cc_start: 0.8187 (mtm180) cc_final: 0.7701 (mtm180) REVERT: R 48 PHE cc_start: 0.8630 (m-10) cc_final: 0.8368 (m-10) REVERT: S 64 LYS cc_start: 0.9196 (mtpp) cc_final: 0.8256 (mtmt) REVERT: T 80 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8462 (tptt) REVERT: T 91 ASP cc_start: 0.8252 (p0) cc_final: 0.7942 (p0) REVERT: T 104 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7008 (p90) REVERT: T 111 ASP cc_start: 0.8000 (t0) cc_final: 0.7699 (t0) REVERT: T 120 MET cc_start: 0.8117 (mtm) cc_final: 0.7827 (mtp) REVERT: T 125 GLU cc_start: 0.8576 (tm-30) cc_final: 0.7715 (tm-30) REVERT: T 142 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8022 (tp-100) REVERT: T 147 TYR cc_start: 0.8697 (t80) cc_final: 0.8408 (t80) REVERT: V 33 ASP cc_start: 0.8938 (t0) cc_final: 0.8581 (m-30) REVERT: X 36 CYS cc_start: 0.8765 (m) cc_final: 0.8194 (m) REVERT: X 44 MET cc_start: 0.8073 (tpp) cc_final: 0.7210 (mmm) REVERT: X 46 CYS cc_start: 0.8711 (m) cc_final: 0.8145 (t) REVERT: X 52 ASP cc_start: 0.8235 (t0) cc_final: 0.7983 (t0) REVERT: X 55 ARG cc_start: 0.8410 (mmm160) cc_final: 0.7980 (mmt180) REVERT: X 80 GLU cc_start: 0.8868 (tp30) cc_final: 0.8478 (mm-30) REVERT: a 60 TYR cc_start: 0.7182 (p90) cc_final: 0.6962 (p90) REVERT: q 53 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8334 (ptpp) REVERT: q 96 ASP cc_start: 0.8802 (m-30) cc_final: 0.8573 (m-30) REVERT: r 40 LYS cc_start: 0.8885 (tttm) cc_final: 0.8478 (tptt) outliers start: 142 outliers final: 81 residues processed: 904 average time/residue: 0.2175 time to fit residues: 322.3015 Evaluate side-chains 825 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 740 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 465 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 GLU Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain b residue 71 GLN Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 346 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 104 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 152 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 69 ASN X 99 HIS Z 24 ASN b 62 ASN q 101 ASN q 123 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.114524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091706 restraints weight = 65859.181| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.23 r_work: 0.3107 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 35413 Z= 0.189 Angle : 0.834 58.779 48017 Z= 0.335 Chirality : 0.045 0.218 5229 Planarity : 0.005 0.132 6085 Dihedral : 9.601 163.480 5020 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.52 % Favored : 96.46 % Rotamer: Outliers : 3.63 % Allowed : 18.46 % Favored : 77.91 % 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: -0.21 (0.13), residues: 4205 helix: 0.84 (0.12), residues: 1884 sheet: -1.04 (0.26), residues: 376 loop : -0.89 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 26 TYR 0.030 0.002 TYR H 247 PHE 0.020 0.002 PHE H 310 TRP 0.035 0.001 TRP E 91 HIS 0.006 0.001 HIS F 303 Details of bonding type rmsd covalent geometry : bond 0.00448 (35373) covalent geometry : angle 0.65975 (47927) SS BOND : bond 0.00238 ( 3) SS BOND : angle 0.64357 ( 6) hydrogen bonds : bond 0.04197 ( 1451) hydrogen bonds : angle 5.18588 ( 4182) metal coordination : bond 0.02291 ( 37) metal coordination : angle 12.21631 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 753 time to evaluate : 1.387 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: C 168 GLU cc_start: 0.8972 (tt0) cc_final: 0.8755 (tt0) REVERT: D 108 LYS cc_start: 0.8922 (ttpp) cc_final: 0.8686 (ttpt) REVERT: D 270 ASN cc_start: 0.8707 (m-40) cc_final: 0.8408 (t0) REVERT: E 143 ASP cc_start: 0.8764 (t0) cc_final: 0.8259 (t0) REVERT: E 165 ASP cc_start: 0.8733 (p0) cc_final: 0.8466 (p0) REVERT: E 188 ASN cc_start: 0.8337 (m-40) cc_final: 0.7974 (m-40) REVERT: E 194 ASP cc_start: 0.8478 (t70) cc_final: 0.8257 (t70) REVERT: F 63 TYR cc_start: 0.8254 (t80) cc_final: 0.8021 (t80) REVERT: F 80 MET cc_start: 0.8986 (mmm) cc_final: 0.8722 (mmm) REVERT: F 131 MET cc_start: 0.8805 (mtm) cc_final: 0.8492 (mtt) REVERT: F 198 VAL cc_start: 0.9217 (t) cc_final: 0.8985 (m) REVERT: F 214 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8088 (mt-10) REVERT: F 292 MET cc_start: 0.8590 (ttm) cc_final: 0.8149 (mtp) REVERT: G 244 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8161 (mt-10) REVERT: G 513 MET cc_start: 0.9034 (tpp) cc_final: 0.8648 (tpp) REVERT: G 660 GLU cc_start: 0.7276 (pp20) cc_final: 0.6951 (pp20) REVERT: H 15 ILE cc_start: 0.9140 (mm) cc_final: 0.8875 (mt) REVERT: H 68 MET cc_start: 0.8202 (tpt) cc_final: 0.7935 (mmm) REVERT: H 199 ASP cc_start: 0.8700 (t0) cc_final: 0.8426 (t0) REVERT: H 224 PHE cc_start: 0.8417 (t80) cc_final: 0.7852 (t80) REVERT: H 255 TYR cc_start: 0.8406 (t80) cc_final: 0.7577 (t80) REVERT: I 40 ASN cc_start: 0.9216 (t0) cc_final: 0.8915 (t0) REVERT: I 49 ASP cc_start: 0.9005 (p0) cc_final: 0.8768 (p0) REVERT: I 98 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7541 (mtt-85) REVERT: I 165 ASP cc_start: 0.8887 (t0) cc_final: 0.8429 (t0) REVERT: I 208 ASP cc_start: 0.8651 (t70) cc_final: 0.8175 (t70) REVERT: P 78 SER cc_start: 0.9027 (m) cc_final: 0.8784 (p) REVERT: P 147 ASN cc_start: 0.8490 (t0) cc_final: 0.8209 (m-40) REVERT: P 295 LEU cc_start: 0.8376 (tt) cc_final: 0.8068 (pt) REVERT: P 336 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: P 355 ARG cc_start: 0.8335 (ptp-170) cc_final: 0.7043 (ttt180) REVERT: Q 55 VAL cc_start: 0.7530 (m) cc_final: 0.7196 (p) REVERT: S 62 GLN cc_start: 0.8692 (mt0) cc_final: 0.8454 (mt0) REVERT: S 64 LYS cc_start: 0.9245 (mtpp) cc_final: 0.8304 (mtmt) REVERT: S 91 MET cc_start: 0.8907 (ttm) cc_final: 0.8421 (ttm) REVERT: T 80 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8417 (tptt) REVERT: T 91 ASP cc_start: 0.8201 (p0) cc_final: 0.7864 (p0) REVERT: T 104 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.6867 (p90) REVERT: T 111 ASP cc_start: 0.8261 (t0) cc_final: 0.7974 (t0) REVERT: T 120 MET cc_start: 0.8129 (mtm) cc_final: 0.7805 (mtp) REVERT: T 125 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7790 (tm-30) REVERT: T 142 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7988 (tp40) REVERT: T 147 TYR cc_start: 0.8663 (t80) cc_final: 0.8347 (t80) REVERT: V 33 ASP cc_start: 0.8983 (t0) cc_final: 0.8579 (m-30) REVERT: W 104 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8719 (t) REVERT: X 36 CYS cc_start: 0.8809 (m) cc_final: 0.8150 (m) REVERT: X 46 CYS cc_start: 0.8772 (m) cc_final: 0.8231 (t) REVERT: X 55 ARG cc_start: 0.8451 (mmm160) cc_final: 0.8017 (mmt180) REVERT: X 108 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8645 (m-30) REVERT: Z 24 ASN cc_start: 0.7567 (t0) cc_final: 0.7211 (t0) REVERT: Z 27 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7273 (ttp80) REVERT: a 60 TYR cc_start: 0.7210 (p90) cc_final: 0.6982 (p90) REVERT: b 44 MET cc_start: 0.8546 (mtp) cc_final: 0.8127 (mtt) REVERT: q 51 ASP cc_start: 0.8500 (t0) cc_final: 0.8063 (t0) REVERT: q 53 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8370 (ptpp) REVERT: r 6 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8074 (mmm160) REVERT: r 30 GLU cc_start: 0.8094 (pm20) cc_final: 0.7739 (pm20) outliers start: 134 outliers final: 91 residues processed: 839 average time/residue: 0.2159 time to fit residues: 297.0373 Evaluate side-chains 817 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 721 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 426 ASP Chi-restraints excluded: chain G residue 465 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 GLU Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 108 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 10 MET Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain b residue 71 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 56 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 377 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 410 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 372 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 68 ASN F 44 ASN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 121 GLN ** S 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 ASN X 69 ASN X 99 HIS q 101 ASN q 123 GLN ** r 52 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 = 0.3591 r_free = 0.3591 target = 0.114801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.092049 restraints weight = 65558.583| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.22 r_work: 0.3110 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35413 Z= 0.160 Angle : 0.822 59.942 48017 Z= 0.325 Chirality : 0.044 0.156 5229 Planarity : 0.005 0.130 6085 Dihedral : 9.471 164.925 5020 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.60 % Allowed : 18.44 % Favored : 77.96 % 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: -0.20 (0.13), residues: 4205 helix: 0.85 (0.12), residues: 1895 sheet: -1.04 (0.26), residues: 366 loop : -0.88 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 41 TYR 0.025 0.002 TYR W 43 PHE 0.026 0.001 PHE X 70 TRP 0.029 0.001 TRP E 91 HIS 0.006 0.001 HIS b 69 Details of bonding type rmsd covalent geometry : bond 0.00380 (35373) covalent geometry : angle 0.64280 (47927) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.74994 ( 6) hydrogen bonds : bond 0.04026 ( 1451) hydrogen bonds : angle 5.09171 ( 4182) metal coordination : bond 0.01990 ( 37) metal coordination : angle 12.26191 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 766 time to evaluate : 1.427 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: A 87 MET cc_start: 0.8965 (tmm) cc_final: 0.8601 (tmm) REVERT: B 72 GLU cc_start: 0.8428 (tp30) cc_final: 0.7504 (tt0) REVERT: C 64 VAL cc_start: 0.9219 (p) cc_final: 0.8977 (t) REVERT: D 108 LYS cc_start: 0.8944 (ttpp) cc_final: 0.8697 (ttpt) REVERT: D 270 ASN cc_start: 0.8736 (m-40) cc_final: 0.8422 (t0) REVERT: E 143 ASP cc_start: 0.8751 (t0) cc_final: 0.8229 (t0) REVERT: E 165 ASP cc_start: 0.8756 (p0) cc_final: 0.8455 (p0) REVERT: E 188 ASN cc_start: 0.8210 (m-40) cc_final: 0.7857 (m-40) REVERT: F 131 MET cc_start: 0.8784 (mtm) cc_final: 0.8497 (mtt) REVERT: F 198 VAL cc_start: 0.9226 (t) cc_final: 0.8985 (m) REVERT: F 214 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8111 (mt-10) REVERT: F 292 MET cc_start: 0.8655 (ttm) cc_final: 0.8170 (mtp) REVERT: G 244 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8217 (mt-10) REVERT: G 513 MET cc_start: 0.9046 (tpp) cc_final: 0.8845 (tpp) REVERT: G 660 GLU cc_start: 0.7385 (pp20) cc_final: 0.7183 (pp20) REVERT: H 15 ILE cc_start: 0.9149 (mm) cc_final: 0.8938 (mt) REVERT: H 24 GLU cc_start: 0.9000 (tt0) cc_final: 0.8783 (tt0) REVERT: H 68 MET cc_start: 0.8277 (tpt) cc_final: 0.8014 (mmm) REVERT: H 199 ASP cc_start: 0.8665 (t0) cc_final: 0.8380 (t0) REVERT: H 224 PHE cc_start: 0.8403 (t80) cc_final: 0.7973 (t80) REVERT: H 255 TYR cc_start: 0.8445 (t80) cc_final: 0.7588 (t80) REVERT: I 40 ASN cc_start: 0.9211 (t0) cc_final: 0.9006 (t0) REVERT: I 76 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7185 (t80) REVERT: I 98 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7666 (mtt-85) REVERT: I 165 ASP cc_start: 0.8886 (t0) cc_final: 0.8396 (t0) REVERT: I 208 ASP cc_start: 0.8652 (t70) cc_final: 0.8295 (t70) REVERT: P 241 TYR cc_start: 0.8365 (t80) cc_final: 0.7829 (t80) REVERT: P 336 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: P 355 ARG cc_start: 0.8408 (ptp-170) cc_final: 0.7089 (ttt180) REVERT: S 62 GLN cc_start: 0.8727 (mt0) cc_final: 0.8448 (mt0) REVERT: S 64 LYS cc_start: 0.9241 (mtpp) cc_final: 0.8272 (mtmt) REVERT: S 85 ASP cc_start: 0.8764 (t0) cc_final: 0.8328 (p0) REVERT: S 91 MET cc_start: 0.8953 (ttm) cc_final: 0.8494 (ttm) REVERT: T 80 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8525 (tptt) REVERT: T 104 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.6771 (p90) REVERT: T 105 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7882 (ptm) REVERT: T 111 ASP cc_start: 0.8261 (t0) cc_final: 0.8060 (t70) REVERT: T 120 MET cc_start: 0.8152 (mtm) cc_final: 0.7814 (mtp) REVERT: T 125 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7802 (tm-30) REVERT: T 142 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8005 (tp40) REVERT: T 147 TYR cc_start: 0.8593 (t80) cc_final: 0.8338 (t80) REVERT: V 33 ASP cc_start: 0.8964 (t0) cc_final: 0.8679 (m-30) REVERT: W 69 MET cc_start: 0.8959 (mmm) cc_final: 0.8700 (mmp) REVERT: X 36 CYS cc_start: 0.8664 (m) cc_final: 0.8147 (m) REVERT: X 37 ASP cc_start: 0.7836 (p0) cc_final: 0.7629 (p0) REVERT: X 46 CYS cc_start: 0.8792 (m) cc_final: 0.8161 (t) REVERT: X 55 ARG cc_start: 0.8381 (mmm160) cc_final: 0.8087 (mmt180) REVERT: X 108 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8587 (m-30) REVERT: Z 24 ASN cc_start: 0.7582 (t0) cc_final: 0.7194 (t0) REVERT: Z 27 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7241 (ttp80) REVERT: a 60 TYR cc_start: 0.7231 (p90) cc_final: 0.6993 (p90) REVERT: a 66 LEU cc_start: 0.9086 (mt) cc_final: 0.8784 (pp) REVERT: b 44 MET cc_start: 0.8563 (mtp) cc_final: 0.8137 (mtt) REVERT: q 51 ASP cc_start: 0.8505 (t0) cc_final: 0.8052 (t0) REVERT: q 53 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8420 (ptpp) REVERT: r 30 GLU cc_start: 0.8171 (pm20) cc_final: 0.7801 (pm20) outliers start: 133 outliers final: 96 residues processed: 847 average time/residue: 0.2094 time to fit residues: 292.7086 Evaluate side-chains 820 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 718 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 426 ASP Chi-restraints excluded: chain G residue 465 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 121 GLN Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 GLU Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 108 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain Z residue 10 MET Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain b residue 71 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 41 LEU Chi-restraints excluded: chain r residue 56 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 172 optimal weight: 8.9990 chunk 230 optimal weight: 0.9980 chunk 295 optimal weight: 3.9990 chunk 341 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 196 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 372 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 132 GLN E 152 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 323 HIS S 62 GLN V 111 GLN X 69 ASN X 99 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN q 123 GLN ** r 52 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 = 0.3599 r_free = 0.3599 target = 0.115602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.092942 restraints weight = 65693.276| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.22 r_work: 0.3123 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35413 Z= 0.144 Angle : 0.823 59.457 48017 Z= 0.322 Chirality : 0.043 0.191 5229 Planarity : 0.005 0.127 6085 Dihedral : 9.304 165.704 5020 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 3.22 % Allowed : 19.79 % Favored : 76.99 % 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: -0.09 (0.13), residues: 4205 helix: 0.94 (0.12), residues: 1892 sheet: -0.94 (0.27), residues: 349 loop : -0.84 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG q 25 TYR 0.025 0.002 TYR W 43 PHE 0.032 0.001 PHE X 70 TRP 0.027 0.001 TRP E 91 HIS 0.006 0.001 HIS F 281 Details of bonding type rmsd covalent geometry : bond 0.00339 (35373) covalent geometry : angle 0.63736 (47927) SS BOND : bond 0.00245 ( 3) SS BOND : angle 0.79218 ( 6) hydrogen bonds : bond 0.03877 ( 1451) hydrogen bonds : angle 5.02495 ( 4182) metal coordination : bond 0.01746 ( 37) metal coordination : angle 12.45316 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 762 time to evaluate : 1.428 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: A 87 MET cc_start: 0.8927 (tmm) cc_final: 0.8563 (tmm) REVERT: C 64 VAL cc_start: 0.9225 (p) cc_final: 0.8988 (t) REVERT: D 108 LYS cc_start: 0.8930 (ttpp) cc_final: 0.8691 (ttpt) REVERT: D 270 ASN cc_start: 0.8655 (m-40) cc_final: 0.8354 (t0) REVERT: E 143 ASP cc_start: 0.8677 (t0) cc_final: 0.8157 (t0) REVERT: E 188 ASN cc_start: 0.8234 (m-40) cc_final: 0.7877 (m-40) REVERT: F 131 MET cc_start: 0.8849 (mtm) cc_final: 0.8563 (mtt) REVERT: F 198 VAL cc_start: 0.9221 (t) cc_final: 0.8994 (m) REVERT: F 214 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8146 (mt-10) REVERT: F 292 MET cc_start: 0.8619 (ttm) cc_final: 0.8163 (mtp) REVERT: G 32 ILE cc_start: 0.9071 (mt) cc_final: 0.8682 (tt) REVERT: G 77 MET cc_start: 0.9056 (tpp) cc_final: 0.8820 (tpt) REVERT: G 244 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8194 (mt-10) REVERT: G 467 LYS cc_start: 0.7812 (mmtm) cc_final: 0.7438 (mmtp) REVERT: G 513 MET cc_start: 0.9039 (tpp) cc_final: 0.8813 (tpp) REVERT: G 661 GLU cc_start: 0.7421 (tt0) cc_final: 0.7041 (tp30) REVERT: H 59 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7525 (tm-30) REVERT: H 199 ASP cc_start: 0.8646 (t0) cc_final: 0.8303 (t0) REVERT: H 214 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7418 (tp30) REVERT: H 224 PHE cc_start: 0.8395 (t80) cc_final: 0.7871 (t80) REVERT: H 255 TYR cc_start: 0.8430 (t80) cc_final: 0.7656 (t80) REVERT: I 76 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7238 (t80) REVERT: I 98 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7628 (mtt-85) REVERT: I 165 ASP cc_start: 0.8826 (t0) cc_final: 0.8385 (t0) REVERT: I 208 ASP cc_start: 0.8673 (t70) cc_final: 0.8370 (t70) REVERT: P 241 TYR cc_start: 0.8383 (t80) cc_final: 0.7811 (t80) REVERT: P 336 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: P 355 ARG cc_start: 0.8419 (ptp-170) cc_final: 0.7430 (mmt-90) REVERT: R 45 ARG cc_start: 0.8230 (mtm180) cc_final: 0.7583 (mtm180) REVERT: S 62 GLN cc_start: 0.8805 (mt0) cc_final: 0.8569 (mt0) REVERT: S 64 LYS cc_start: 0.9278 (mtpp) cc_final: 0.8340 (mtmt) REVERT: S 85 ASP cc_start: 0.8724 (t0) cc_final: 0.8299 (p0) REVERT: S 91 MET cc_start: 0.8933 (ttm) cc_final: 0.8489 (ttm) REVERT: T 91 ASP cc_start: 0.8344 (p0) cc_final: 0.8041 (p0) REVERT: T 104 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.6730 (p90) REVERT: T 105 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7862 (ptm) REVERT: T 111 ASP cc_start: 0.8327 (t0) cc_final: 0.8063 (t0) REVERT: T 120 MET cc_start: 0.8150 (mtm) cc_final: 0.7767 (mtp) REVERT: T 125 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8108 (tm-30) REVERT: T 142 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8088 (tp40) REVERT: T 147 TYR cc_start: 0.8547 (t80) cc_final: 0.8302 (t80) REVERT: V 33 ASP cc_start: 0.8963 (t0) cc_final: 0.8678 (m-30) REVERT: W 43 TYR cc_start: 0.9319 (t80) cc_final: 0.8892 (t80) REVERT: W 105 HIS cc_start: 0.8922 (m90) cc_final: 0.8680 (m90) REVERT: X 36 CYS cc_start: 0.8634 (m) cc_final: 0.8118 (m) REVERT: X 108 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8569 (m-30) REVERT: Z 24 ASN cc_start: 0.7699 (t0) cc_final: 0.7307 (t0) REVERT: Z 27 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7236 (ttp80) REVERT: Z 90 ASN cc_start: 0.8809 (m-40) cc_final: 0.8310 (m110) REVERT: Z 94 GLU cc_start: 0.8694 (tt0) cc_final: 0.8456 (tt0) REVERT: a 60 TYR cc_start: 0.7227 (p90) cc_final: 0.6991 (p90) REVERT: a 66 LEU cc_start: 0.9029 (mt) cc_final: 0.8720 (pp) REVERT: b 44 MET cc_start: 0.8552 (mtp) cc_final: 0.8145 (mtt) REVERT: b 71 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8413 (mt0) REVERT: q 53 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8493 (mtmm) REVERT: r 6 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8349 (mmm160) REVERT: r 30 GLU cc_start: 0.8171 (pm20) cc_final: 0.7782 (pm20) outliers start: 119 outliers final: 84 residues processed: 835 average time/residue: 0.2124 time to fit residues: 290.7787 Evaluate side-chains 807 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 716 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 GLU Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 108 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain b residue 71 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 56 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 172 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 388 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 367 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 152 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN P 166 HIS Q 86 ASN ** S 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 69 ASN X 99 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091457 restraints weight = 65840.564| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.22 r_work: 0.3101 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 35413 Z= 0.175 Angle : 0.841 59.909 48017 Z= 0.332 Chirality : 0.044 0.193 5229 Planarity : 0.005 0.128 6085 Dihedral : 9.234 166.369 5020 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 3.25 % Allowed : 19.92 % Favored : 76.83 % 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: -0.12 (0.13), residues: 4205 helix: 0.92 (0.12), residues: 1900 sheet: -0.99 (0.27), residues: 359 loop : -0.86 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 41 TYR 0.032 0.002 TYR W 43 PHE 0.031 0.002 PHE X 70 TRP 0.031 0.001 TRP E 91 HIS 0.007 0.001 HIS b 69 Details of bonding type rmsd covalent geometry : bond 0.00418 (35373) covalent geometry : angle 0.65676 (47927) SS BOND : bond 0.00239 ( 3) SS BOND : angle 0.75352 ( 6) hydrogen bonds : bond 0.03942 ( 1451) hydrogen bonds : angle 5.03346 ( 4182) metal coordination : bond 0.02161 ( 37) metal coordination : angle 12.59281 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 738 time to evaluate : 1.448 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: A 87 MET cc_start: 0.8938 (tmm) cc_final: 0.8588 (tmm) REVERT: B 72 GLU cc_start: 0.8399 (tp30) cc_final: 0.7477 (tt0) REVERT: C 64 VAL cc_start: 0.9245 (p) cc_final: 0.8992 (t) REVERT: D 108 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8688 (ttpt) REVERT: D 270 ASN cc_start: 0.8671 (m-40) cc_final: 0.8431 (t0) REVERT: D 443 MET cc_start: 0.8412 (mtm) cc_final: 0.8155 (mtt) REVERT: E 143 ASP cc_start: 0.8691 (t0) cc_final: 0.8167 (t0) REVERT: E 188 ASN cc_start: 0.8211 (m-40) cc_final: 0.7834 (m-40) REVERT: F 198 VAL cc_start: 0.9216 (t) cc_final: 0.8968 (m) REVERT: F 208 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8405 (tm-30) REVERT: F 214 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8152 (mt-10) REVERT: G 244 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8265 (mt-10) REVERT: G 300 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: G 467 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7402 (mmtp) REVERT: G 513 MET cc_start: 0.8976 (tpp) cc_final: 0.8764 (tpp) REVERT: G 661 GLU cc_start: 0.7399 (tt0) cc_final: 0.7078 (tp30) REVERT: H 59 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7607 (tm-30) REVERT: H 199 ASP cc_start: 0.8600 (t0) cc_final: 0.8342 (t0) REVERT: H 214 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7628 (tp30) REVERT: H 224 PHE cc_start: 0.8336 (t80) cc_final: 0.7684 (t80) REVERT: H 228 TYR cc_start: 0.8870 (m-10) cc_final: 0.8635 (m-10) REVERT: H 255 TYR cc_start: 0.8498 (t80) cc_final: 0.7700 (t80) REVERT: I 76 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7250 (t80) REVERT: I 98 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7609 (mtt-85) REVERT: I 165 ASP cc_start: 0.8889 (t0) cc_final: 0.8394 (t0) REVERT: I 208 ASP cc_start: 0.8699 (t70) cc_final: 0.8424 (t70) REVERT: P 241 TYR cc_start: 0.8409 (t80) cc_final: 0.7986 (t80) REVERT: P 336 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: P 355 ARG cc_start: 0.8422 (ptp-170) cc_final: 0.7147 (ttt180) REVERT: R 45 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7588 (mtm180) REVERT: S 64 LYS cc_start: 0.9309 (mtpp) cc_final: 0.8343 (mtmt) REVERT: S 85 ASP cc_start: 0.8761 (t0) cc_final: 0.8313 (p0) REVERT: S 91 MET cc_start: 0.8954 (ttm) cc_final: 0.8526 (ttm) REVERT: T 91 ASP cc_start: 0.8399 (p0) cc_final: 0.8111 (p0) REVERT: T 104 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6635 (p90) REVERT: T 105 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7751 (ptm) REVERT: T 111 ASP cc_start: 0.8488 (t0) cc_final: 0.8187 (t0) REVERT: T 120 MET cc_start: 0.8124 (mtm) cc_final: 0.7736 (mtm) REVERT: T 123 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7510 (mp0) REVERT: T 125 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7859 (tm-30) REVERT: T 142 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8039 (tp40) REVERT: T 147 TYR cc_start: 0.8470 (t80) cc_final: 0.8009 (t80) REVERT: V 33 ASP cc_start: 0.8983 (t0) cc_final: 0.8657 (m-30) REVERT: X 36 CYS cc_start: 0.8646 (m) cc_final: 0.8117 (m) REVERT: X 46 CYS cc_start: 0.8870 (m) cc_final: 0.8314 (t) REVERT: X 108 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8591 (m-30) REVERT: X 140 ASN cc_start: 0.8117 (t0) cc_final: 0.7423 (p0) REVERT: Z 24 ASN cc_start: 0.7712 (t0) cc_final: 0.7327 (t0) REVERT: Z 27 ARG cc_start: 0.7563 (ttp80) cc_final: 0.7212 (ttp80) REVERT: Z 90 ASN cc_start: 0.8804 (m-40) cc_final: 0.8242 (m110) REVERT: a 60 TYR cc_start: 0.7300 (p90) cc_final: 0.7061 (p90) REVERT: a 66 LEU cc_start: 0.9058 (mt) cc_final: 0.8757 (pp) REVERT: b 44 MET cc_start: 0.8588 (mtp) cc_final: 0.8189 (mtt) REVERT: b 71 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8542 (mt0) REVERT: q 53 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8506 (mtmm) REVERT: r 30 GLU cc_start: 0.8223 (pm20) cc_final: 0.7814 (pm20) outliers start: 120 outliers final: 95 residues processed: 813 average time/residue: 0.2129 time to fit residues: 285.1661 Evaluate side-chains 815 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 712 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 GLN Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 465 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 196 LYS Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 121 GLN Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 GLU Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 112 LYS Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 108 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain b residue 71 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 56 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 132 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 339 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 296 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN X 69 ASN X 99 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.091187 restraints weight = 65764.149| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.23 r_work: 0.3097 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35413 Z= 0.170 Angle : 0.842 60.458 48017 Z= 0.333 Chirality : 0.044 0.192 5229 Planarity : 0.005 0.127 6085 Dihedral : 9.163 167.340 5020 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 3.44 % Allowed : 19.73 % Favored : 76.83 % 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: -0.11 (0.13), residues: 4205 helix: 0.92 (0.12), residues: 1907 sheet: -0.90 (0.27), residues: 350 loop : -0.87 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 41 TYR 0.034 0.002 TYR W 43 PHE 0.027 0.002 PHE X 70 TRP 0.030 0.001 TRP E 91 HIS 0.006 0.001 HIS F 281 Details of bonding type rmsd covalent geometry : bond 0.00405 (35373) covalent geometry : angle 0.65644 (47927) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.74324 ( 6) hydrogen bonds : bond 0.03920 ( 1451) hydrogen bonds : angle 4.99890 ( 4182) metal coordination : bond 0.02059 ( 37) metal coordination : angle 12.60729 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 724 time to evaluate : 1.344 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: B 72 GLU cc_start: 0.8376 (tp30) cc_final: 0.7442 (tt0) REVERT: C 64 VAL cc_start: 0.9223 (p) cc_final: 0.8995 (t) REVERT: D 108 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8682 (ttpt) REVERT: D 270 ASN cc_start: 0.8671 (m-40) cc_final: 0.8437 (t0) REVERT: E 143 ASP cc_start: 0.8673 (t0) cc_final: 0.8161 (t0) REVERT: E 188 ASN cc_start: 0.8270 (m-40) cc_final: 0.7903 (m-40) REVERT: F 198 VAL cc_start: 0.9144 (t) cc_final: 0.8870 (m) REVERT: F 208 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8429 (tm-30) REVERT: G 54 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8325 (tp30) REVERT: G 77 MET cc_start: 0.9092 (tpp) cc_final: 0.8829 (tpt) REVERT: G 244 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8271 (mt-10) REVERT: G 300 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: G 513 MET cc_start: 0.8968 (tpp) cc_final: 0.8768 (tpp) REVERT: G 661 GLU cc_start: 0.7358 (tt0) cc_final: 0.7066 (tp30) REVERT: H 59 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7762 (tm-30) REVERT: H 152 SER cc_start: 0.9173 (m) cc_final: 0.8618 (t) REVERT: H 199 ASP cc_start: 0.8566 (t0) cc_final: 0.8225 (t0) REVERT: H 224 PHE cc_start: 0.8311 (t80) cc_final: 0.7736 (t80) REVERT: H 228 TYR cc_start: 0.8887 (m-10) cc_final: 0.8663 (m-10) REVERT: H 255 TYR cc_start: 0.8525 (t80) cc_final: 0.7768 (t80) REVERT: I 76 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7249 (t80) REVERT: I 98 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7608 (mtt-85) REVERT: I 165 ASP cc_start: 0.8936 (t0) cc_final: 0.8428 (t0) REVERT: I 208 ASP cc_start: 0.8701 (t70) cc_final: 0.8445 (t70) REVERT: P 121 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.8016 (mm110) REVERT: P 241 TYR cc_start: 0.8351 (t80) cc_final: 0.7944 (t80) REVERT: P 336 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: P 355 ARG cc_start: 0.8429 (ptp-170) cc_final: 0.7153 (ttt180) REVERT: R 45 ARG cc_start: 0.8196 (mtm180) cc_final: 0.7527 (mtm180) REVERT: R 48 PHE cc_start: 0.8436 (m-10) cc_final: 0.8128 (m-10) REVERT: S 64 LYS cc_start: 0.9321 (mtpp) cc_final: 0.8299 (mtmt) REVERT: S 85 ASP cc_start: 0.8754 (t0) cc_final: 0.8298 (p0) REVERT: S 91 MET cc_start: 0.9009 (ttm) cc_final: 0.8593 (ttm) REVERT: T 91 ASP cc_start: 0.8465 (p0) cc_final: 0.8055 (p0) REVERT: T 104 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7181 (p90) REVERT: T 105 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7867 (ptm) REVERT: T 120 MET cc_start: 0.8427 (mtm) cc_final: 0.7988 (mtp) REVERT: T 125 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7879 (tm-30) REVERT: T 142 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8073 (tp40) REVERT: T 147 TYR cc_start: 0.8358 (t80) cc_final: 0.8117 (t80) REVERT: V 33 ASP cc_start: 0.8962 (t0) cc_final: 0.8660 (m-30) REVERT: X 36 CYS cc_start: 0.8614 (m) cc_final: 0.8093 (m) REVERT: X 46 CYS cc_start: 0.8883 (m) cc_final: 0.8397 (t) REVERT: X 108 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8591 (m-30) REVERT: Z 24 ASN cc_start: 0.7680 (t0) cc_final: 0.6977 (t0) REVERT: Z 76 GLN cc_start: 0.8978 (tp40) cc_final: 0.8772 (tp-100) REVERT: Z 90 ASN cc_start: 0.8887 (m-40) cc_final: 0.8340 (m110) REVERT: a 60 TYR cc_start: 0.7329 (p90) cc_final: 0.7092 (p90) REVERT: a 66 LEU cc_start: 0.9040 (mt) cc_final: 0.8752 (pp) REVERT: b 44 MET cc_start: 0.8570 (mtp) cc_final: 0.8176 (mtt) REVERT: q 53 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8649 (pttp) REVERT: q 114 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7364 (mptt) REVERT: r 30 GLU cc_start: 0.8209 (pm20) cc_final: 0.7791 (pm20) outliers start: 127 outliers final: 95 residues processed: 802 average time/residue: 0.2103 time to fit residues: 277.9688 Evaluate side-chains 808 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 705 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 GLN Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 426 ASP Chi-restraints excluded: chain G residue 465 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 121 GLN Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 GLU Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 40 ARG Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 108 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain q residue 101 ASN Chi-restraints excluded: chain r residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 184 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 369 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 161 optimal weight: 0.2980 chunk 377 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN ** S 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN W 73 ASN X 69 ASN X 99 HIS q 101 ASN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092865 restraints weight = 65764.373| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.25 r_work: 0.3125 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35413 Z= 0.136 Angle : 0.839 61.636 48017 Z= 0.332 Chirality : 0.044 0.352 5229 Planarity : 0.005 0.126 6085 Dihedral : 9.050 167.752 5020 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 2.87 % Allowed : 20.41 % Favored : 76.72 % 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: -0.07 (0.13), residues: 4205 helix: 0.97 (0.12), residues: 1909 sheet: -0.95 (0.27), residues: 356 loop : -0.85 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 26 TYR 0.028 0.001 TYR W 43 PHE 0.035 0.001 PHE A 62 TRP 0.034 0.001 TRP E 91 HIS 0.006 0.001 HIS F 281 Details of bonding type rmsd covalent geometry : bond 0.00315 (35373) covalent geometry : angle 0.66001 (47927) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.71884 ( 6) hydrogen bonds : bond 0.03780 ( 1451) hydrogen bonds : angle 4.95030 ( 4182) metal coordination : bond 0.01525 ( 37) metal coordination : angle 12.41466 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 740 time to evaluate : 1.371 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: B 72 GLU cc_start: 0.8384 (tp30) cc_final: 0.7469 (tt0) REVERT: C 64 VAL cc_start: 0.9206 (p) cc_final: 0.8967 (t) REVERT: D 108 LYS cc_start: 0.8922 (ttpp) cc_final: 0.8684 (ttpt) REVERT: D 270 ASN cc_start: 0.8675 (m-40) cc_final: 0.8443 (t0) REVERT: D 455 ASP cc_start: 0.7723 (t0) cc_final: 0.7485 (t0) REVERT: E 143 ASP cc_start: 0.8673 (t0) cc_final: 0.8306 (t0) REVERT: E 188 ASN cc_start: 0.8263 (m-40) cc_final: 0.7878 (m-40) REVERT: F 198 VAL cc_start: 0.9161 (t) cc_final: 0.8883 (m) REVERT: F 208 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8439 (tm-30) REVERT: F 214 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8289 (mm-30) REVERT: F 292 MET cc_start: 0.8476 (mtp) cc_final: 0.8238 (mtp) REVERT: G 77 MET cc_start: 0.9044 (tpp) cc_final: 0.8773 (tpt) REVERT: G 244 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8143 (mt-10) REVERT: G 300 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: G 661 GLU cc_start: 0.7323 (tt0) cc_final: 0.7111 (tp30) REVERT: H 80 THR cc_start: 0.9130 (m) cc_final: 0.8915 (m) REVERT: H 199 ASP cc_start: 0.8536 (t0) cc_final: 0.8220 (t0) REVERT: H 255 TYR cc_start: 0.8438 (t80) cc_final: 0.7864 (t80) REVERT: I 65 GLU cc_start: 0.7341 (tp30) cc_final: 0.7058 (tp30) REVERT: I 76 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7302 (t80) REVERT: I 98 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7612 (mtt-85) REVERT: I 165 ASP cc_start: 0.8877 (t0) cc_final: 0.8419 (t0) REVERT: I 211 TYR cc_start: 0.8224 (m-80) cc_final: 0.7282 (m-80) REVERT: P 121 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8073 (mm110) REVERT: P 241 TYR cc_start: 0.8334 (t80) cc_final: 0.7910 (t80) REVERT: P 336 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: P 355 ARG cc_start: 0.8400 (ptp-170) cc_final: 0.7140 (ttt180) REVERT: R 45 ARG cc_start: 0.8241 (mtm180) cc_final: 0.7568 (mtm180) REVERT: S 27 SER cc_start: 0.7426 (OUTLIER) cc_final: 0.6927 (p) REVERT: S 64 LYS cc_start: 0.9312 (mtpp) cc_final: 0.8291 (mtmt) REVERT: S 85 ASP cc_start: 0.8738 (t0) cc_final: 0.8252 (p0) REVERT: S 91 MET cc_start: 0.8958 (ttm) cc_final: 0.8550 (ttm) REVERT: T 91 ASP cc_start: 0.8488 (p0) cc_final: 0.8154 (p0) REVERT: T 104 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7177 (p90) REVERT: T 105 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7844 (ptm) REVERT: T 120 MET cc_start: 0.8350 (mtm) cc_final: 0.7816 (mtp) REVERT: T 125 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7850 (tm-30) REVERT: T 142 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7939 (tp40) REVERT: V 33 ASP cc_start: 0.8946 (t0) cc_final: 0.8666 (m-30) REVERT: X 36 CYS cc_start: 0.8575 (m) cc_final: 0.8054 (m) REVERT: X 46 CYS cc_start: 0.8904 (m) cc_final: 0.8357 (t) REVERT: X 108 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8607 (m-30) REVERT: Z 24 ASN cc_start: 0.7695 (t0) cc_final: 0.7014 (t0) REVERT: Z 76 GLN cc_start: 0.8944 (tp40) cc_final: 0.8579 (tp-100) REVERT: Z 90 ASN cc_start: 0.8848 (m-40) cc_final: 0.8313 (m110) REVERT: Z 94 GLU cc_start: 0.8646 (tt0) cc_final: 0.7698 (tp30) REVERT: a 60 TYR cc_start: 0.7291 (p90) cc_final: 0.7051 (p90) REVERT: a 66 LEU cc_start: 0.8997 (mt) cc_final: 0.8716 (pp) REVERT: b 44 MET cc_start: 0.8529 (mtp) cc_final: 0.8159 (mtt) REVERT: q 53 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8644 (pttp) REVERT: r 30 GLU cc_start: 0.8183 (pm20) cc_final: 0.7750 (pm20) outliers start: 106 outliers final: 79 residues processed: 803 average time/residue: 0.2135 time to fit residues: 282.9686 Evaluate side-chains 803 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 715 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 GLN Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 57 MET Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 121 GLN Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 GLU Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 108 ASP Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 71 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain q residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 195 optimal weight: 0.0980 chunk 354 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 176 optimal weight: 0.9990 chunk 361 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 315 optimal weight: 0.3980 chunk 276 optimal weight: 3.9990 chunk 249 optimal weight: 0.0270 chunk 351 optimal weight: 2.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN V 50 GLN W 73 ASN X 69 ASN X 99 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094046 restraints weight = 65461.431| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.25 r_work: 0.3143 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 35413 Z= 0.129 Angle : 0.830 62.436 48017 Z= 0.328 Chirality : 0.043 0.299 5229 Planarity : 0.005 0.124 6085 Dihedral : 8.939 168.002 5020 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 2.49 % Allowed : 21.12 % Favored : 76.39 % 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: -0.00 (0.13), residues: 4205 helix: 1.03 (0.12), residues: 1903 sheet: -0.85 (0.27), residues: 349 loop : -0.84 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 26 TYR 0.017 0.001 TYR P 271 PHE 0.030 0.001 PHE X 70 TRP 0.041 0.001 TRP E 91 HIS 0.007 0.001 HIS P 122 Details of bonding type rmsd covalent geometry : bond 0.00296 (35373) covalent geometry : angle 0.65183 (47927) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.75003 ( 6) hydrogen bonds : bond 0.03696 ( 1451) hydrogen bonds : angle 4.90582 ( 4182) metal coordination : bond 0.01295 ( 37) metal coordination : angle 12.28280 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10866.05 seconds wall clock time: 186 minutes 42.81 seconds (11202.81 seconds total)