Starting phenix.real_space_refine on Tue May 5 22:33:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iba_35337/05_2026/8iba_35337_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iba_35337/05_2026/8iba_35337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iba_35337/05_2026/8iba_35337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iba_35337/05_2026/8iba_35337.map" model { file = "/net/cci-nas-00/data/ceres_data/8iba_35337/05_2026/8iba_35337_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iba_35337/05_2026/8iba_35337_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.088 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 12 5.49 5 S 245 5.16 5 C 21776 2.51 5 N 5777 2.21 5 O 6167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34006 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 762 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} 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: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3095 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 21, 'TRANS': 364} 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: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2525 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 22, 'TRANS': 293} Chain breaks: 2 Chain: "I" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1398 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 1 Chain: "P" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2730 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} 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: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain breaks: 1 Chain: "r" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 413 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain breaks: 1 Chain: "s" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 226 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'PC1': 1, 'SF4': 1, 'UQ1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'UQ9': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 109 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 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: "a" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1014 SG CYS B 99 81.326 59.487 104.958 1.00 29.52 S ATOM 1517 SG CYS B 164 78.600 56.073 110.023 1.00 28.96 S ATOM 1747 SG CYS B 194 83.746 55.923 109.223 1.00 29.28 S ATOM 1020 SG CYS B 100 80.016 55.511 104.210 1.00 30.11 S ATOM 7534 SG CYS E 134 141.472 51.525 151.059 1.00 56.01 S ATOM 7568 SG CYS E 139 143.949 53.140 150.285 1.00 56.50 S ATOM 7852 SG CYS E 175 139.111 55.032 153.667 1.00 54.42 S ATOM 7875 SG CYS E 179 142.412 56.708 153.731 1.00 57.95 S ATOM 11405 SG CYS F 425 122.793 60.793 153.944 1.00 45.60 S ATOM 11083 SG CYS F 385 122.781 58.222 148.192 1.00 39.95 S ATOM 11063 SG CYS F 382 118.534 59.423 150.477 1.00 40.29 S ATOM 11044 SG CYS F 379 120.519 55.403 153.389 1.00 43.09 S ATOM 12453 SG CYS G 131 102.220 48.067 137.260 1.00 31.31 S ATOM 12432 SG CYS G 128 104.196 51.838 132.592 1.00 30.26 S ATOM 12493 SG CYS G 137 101.903 53.991 138.600 1.00 33.13 S ATOM 13178 SG CYS G 226 103.823 48.196 145.834 1.00 34.31 S ATOM 12849 SG CYS G 182 107.013 46.601 151.586 1.00 36.31 S ATOM 12825 SG CYS G 179 106.376 52.144 148.969 1.00 35.62 S ATOM 12802 SG CYS G 176 109.796 47.838 146.532 1.00 34.05 S ATOM 11939 SG CYS G 64 107.807 58.211 150.885 1.00 35.53 S ATOM 12025 SG CYS G 75 108.521 60.229 149.185 1.00 36.47 S ATOM 12050 SG CYS G 78 107.434 64.709 151.242 1.00 36.76 S ATOM 12151 SG CYS G 92 107.236 62.850 154.451 1.00 39.04 S ATOM 20166 SG CYS I 123 87.739 50.912 118.359 1.00 27.30 S ATOM 20392 SG CYS I 152 87.475 49.675 113.264 1.00 27.39 S ATOM 20439 SG CYS I 158 93.143 49.867 115.347 1.00 26.60 S ATOM 20418 SG CYS I 155 90.033 54.281 114.978 1.00 27.04 S ATOM 20115 SG CYS I 116 97.614 46.971 125.762 1.00 29.24 S ATOM 20138 SG CYS I 119 93.235 46.597 122.427 1.00 28.85 S ATOM 20096 SG CYS I 113 96.458 41.790 122.570 1.00 28.61 S ATOM 20468 SG CYS I 162 99.340 46.366 120.395 1.00 28.07 S ATOM 24977 SG CYS R 79 112.867 39.723 125.062 1.00 32.60 S ATOM 25153 SG CYS R 104 110.418 38.313 126.538 1.00 32.49 S ATOM 25175 SG CYS R 107 109.733 38.915 123.107 1.00 30.78 S Time building chain proxies: 7.68, per 1000 atoms: 0.23 Number of scatterers: 34006 At special positions: 0 Unit cell: (169.4, 128.7, 201.3, 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 245 16.00 P 12 15.00 O 6167 8.00 N 5777 7.00 C 21776 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 46 " - pdb=" SG CYS X 56 " distance=2.03 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: 3.48 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " 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 303 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 303 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 304 " pdb="FE3 SF4 I 304 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 304 " - pdb=" SG CYS I 162 " pdb="FE1 SF4 I 304 " - pdb=" SG CYS I 116 " pdb="FE2 SF4 I 304 " - pdb=" SG CYS I 119 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7840 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 32 sheets defined 49.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' 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 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.585A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.588A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (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: 3.602A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.321A 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: 3.647A 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: 3.853A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.296A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.771A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.861A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.893A 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: 3.858A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 3.691A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.670A 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: 3.530A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.259A 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: 3.621A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 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: 3.525A 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: 3.683A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (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 removed outlier: 3.558A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.294A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) 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: 3.921A 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: 3.516A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.636A pdb=" N GLY F 188 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.832A 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: 8.645A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.861A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 335 removed outlier: 4.062A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.604A 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: 3.546A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.662A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.645A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.349A 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: 3.775A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.727A 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 139 through 146 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.932A 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: 3.820A 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: 3.671A 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: 3.636A 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 631 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: 3.523A 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: 3.750A 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: 3.574A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 85 removed outlier: 3.740A pdb=" N THR H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 124 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: 4.552A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.855A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.735A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 214 removed outlier: 3.899A pdb=" N GLU H 214 " --> pdb=" O PHE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.538A 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: 3.529A 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: 3.865A 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: 5.144A 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 96 removed outlier: 4.872A pdb=" N HIS P 93 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) 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: 3.755A pdb=" N ARG P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.621A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 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: 5.688A 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 360 through 364 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.412A 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 164 removed outlier: 4.200A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'R' and resid 44 through 49 Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.549A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 59 through 64' Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 6.447A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.501A 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 removed outlier: 3.811A pdb=" N TYR T 90 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 127 Processing helix chain 'T' and resid 133 through 138 removed outlier: 3.625A 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: 3.676A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.586A 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: 3.529A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.625A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 51 Processing helix chain 'X' and resid 52 through 55 Processing helix chain 'X' and resid 56 through 77 Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.944A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'X' and resid 140 through 144 removed outlier: 4.464A pdb=" N SER X 144 " --> pdb=" O PRO X 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix removed outlier: 3.905A pdb=" N MET Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.499A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.598A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.536A 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: 3.758A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.844A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 removed outlier: 3.663A pdb=" N LEU q 23 " --> pdb=" O GLY q 19 " (cutoff:3.500A) 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: 4.627A 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 's' and resid 43 through 54 removed outlier: 4.203A 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 94 removed outlier: 6.373A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 77 removed outlier: 3.523A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU C 83 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LYS C 143 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE C 85 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.149A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.563A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.255A pdb=" N ARG D 96 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 100 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 108 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.373A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 397 through 401 removed outlier: 3.500A pdb=" N PHE D 407 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.151A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.808A 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 89 through 90 removed outlier: 3.867A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) 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: 6.313A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.639A 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: 6.786A 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: 7.516A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.091A 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: 5.423A 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: 6.359A 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 76 through 79 removed outlier: 4.031A pdb=" N VAL R 91 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.506A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 53 through 56 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 129 through 130 Processing sheet with id=AD5, first strand: chain 'q' and resid 37 through 42 removed outlier: 6.240A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) 1432 hydrogen bonds defined for protein. 4152 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: 7.76 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.36: 11011 1.36 - 1.57: 23311 1.57 - 1.79: 215 1.79 - 2.01: 203 2.01 - 2.23: 80 Bond restraints: 34820 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.647 0.731 2.00e-02 2.50e+03 1.34e+03 bond pdb=" N PRO R 89 " pdb=" CD PRO R 89 " ideal model delta sigma weight residual 1.473 1.261 0.212 1.40e-02 5.10e+03 2.29e+02 bond pdb=" N PRO q 139 " pdb=" CD PRO q 139 " ideal model delta sigma weight residual 1.473 1.286 0.187 1.40e-02 5.10e+03 1.78e+02 bond pdb=" N PRO P 371 " pdb=" CD PRO P 371 " ideal model delta sigma weight residual 1.473 1.654 -0.181 1.40e-02 5.10e+03 1.68e+02 bond pdb=" N PRO G 532 " pdb=" CD PRO G 532 " ideal model delta sigma weight residual 1.473 1.297 0.176 1.40e-02 5.10e+03 1.58e+02 ... (remaining 34815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.68: 46376 6.68 - 13.35: 633 13.35 - 20.03: 160 20.03 - 26.70: 5 26.70 - 33.38: 2 Bond angle restraints: 47176 Sorted by residual: angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" CB VAL D 142 " ideal model delta sigma weight residual 110.65 132.44 -21.79 1.13e+00 7.83e-01 3.72e+02 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 110.42 92.53 17.89 9.40e-01 1.13e+00 3.62e+02 angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.00 25.64 1.52e+00 4.33e-01 2.84e+02 angle pdb=" N CYS F 125 " pdb=" CA CYS F 125 " pdb=" C CYS F 125 " ideal model delta sigma weight residual 113.17 93.48 19.69 1.26e+00 6.30e-01 2.44e+02 angle pdb=" N CYS F 332 " pdb=" CA CYS F 332 " pdb=" C CYS F 332 " ideal model delta sigma weight residual 111.02 129.99 -18.97 1.22e+00 6.72e-01 2.42e+02 ... (remaining 47171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.58: 20284 27.58 - 55.15: 645 55.15 - 82.73: 80 82.73 - 110.31: 7 110.31 - 137.89: 4 Dihedral angle restraints: 21020 sinusoidal: 8860 harmonic: 12160 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 -101.21 -21.39 0 2.50e+00 1.60e-01 7.32e+01 dihedral pdb=" C PHE a 3 " pdb=" N PHE a 3 " pdb=" CA PHE a 3 " pdb=" CB PHE a 3 " ideal model delta harmonic sigma weight residual -122.60 -101.68 -20.92 0 2.50e+00 1.60e-01 7.01e+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 93.00 161.52 -68.52 1 1.00e+01 1.00e-02 6.08e+01 ... (remaining 21017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 4547 0.184 - 0.367: 529 0.367 - 0.551: 47 0.551 - 0.734: 5 0.734 - 0.918: 24 Chirality restraints: 5152 Sorted by residual: chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.92 2.00e-01 2.50e+01 2.11e+01 chirality pdb="FE3 SF4 I 304 " pdb=" S1 SF4 I 304 " pdb=" S2 SF4 I 304 " pdb=" S4 SF4 I 304 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb="FE3 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.65 -0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 5149 not shown) Planarity restraints: 5985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ9 H 400 " -0.343 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C18 UQ9 H 400 " 0.509 2.00e-02 2.50e+03 pdb=" C19 UQ9 H 400 " 0.109 2.00e-02 2.50e+03 pdb=" C20 UQ9 H 400 " -0.135 2.00e-02 2.50e+03 pdb=" C21 UQ9 H 400 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 UQ9 H 400 " -0.303 2.00e-02 2.50e+03 2.57e-01 8.28e+02 pdb=" C23 UQ9 H 400 " 0.438 2.00e-02 2.50e+03 pdb=" C24 UQ9 H 400 " 0.098 2.00e-02 2.50e+03 pdb=" C25 UQ9 H 400 " -0.045 2.00e-02 2.50e+03 pdb=" C26 UQ9 H 400 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 400 " 0.023 2.00e-02 2.50e+03 1.60e-01 7.72e+02 pdb=" C1M UQ9 H 400 " 0.111 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 400 " -0.021 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 400 " -0.043 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 400 " 0.079 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 400 " -0.094 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 400 " -0.004 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 400 " 0.081 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 400 " -0.029 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 400 " -0.173 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 400 " 0.381 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 400 " -0.310 2.00e-02 2.50e+03 ... (remaining 5982 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 86 2.38 - 3.01: 22906 3.01 - 3.64: 53238 3.64 - 4.27: 84095 4.27 - 4.90: 135822 Nonbonded interactions: 296147 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.755 3.040 nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.941 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.970 3.040 nonbonded pdb=" OD1 ASN P 376 " pdb=" N TYR P 377 " model vdw 1.980 3.120 nonbonded pdb=" O ASN H 97 " pdb=" OD1 ASN H 97 " model vdw 1.983 3.040 ... (remaining 296142 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 42.190 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.023 1.141 34860 Z= 1.077 Angle : 2.286 52.575 47266 Z= 1.525 Chirality : 0.132 0.918 5152 Planarity : 0.010 0.292 5985 Dihedral : 13.278 137.887 13171 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 43.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.63 % Favored : 94.22 % Rotamer: Outliers : 0.25 % Allowed : 7.68 % Favored : 92.08 % Cbeta Deviations : 1.94 % 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: -2.09 (0.12), residues: 4136 helix: -0.78 (0.11), residues: 1797 sheet: -1.07 (0.29), residues: 339 loop : -2.00 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 333 TYR 0.046 0.002 TYR B 112 PHE 0.052 0.002 PHE a 3 TRP 0.034 0.002 TRP G 285 HIS 0.017 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.01505 (34820) covalent geometry : angle 2.15896 (47176) SS BOND : bond 0.00762 ( 3) SS BOND : angle 2.18971 ( 6) hydrogen bonds : bond 0.24511 ( 1432) hydrogen bonds : angle 8.95573 ( 4152) metal coordination : bond 0.52308 ( 37) metal coordination : angle 17.98670 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1425 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.7621 (m-40) cc_final: 0.7402 (t0) REVERT: A 13 LEU cc_start: 0.8684 (tp) cc_final: 0.8465 (tt) REVERT: A 24 LEU cc_start: 0.8685 (tm) cc_final: 0.8378 (tt) REVERT: B 93 MET cc_start: 0.8131 (ttp) cc_final: 0.7851 (ttp) REVERT: B 147 LYS cc_start: 0.8178 (tptt) cc_final: 0.7939 (ttpt) REVERT: B 171 TYR cc_start: 0.8592 (m-80) cc_final: 0.8188 (m-80) REVERT: B 213 LYS cc_start: 0.8544 (tttt) cc_final: 0.8281 (ttmt) REVERT: C 172 MET cc_start: 0.8589 (mmt) cc_final: 0.8230 (mmt) REVERT: C 188 THR cc_start: 0.8855 (p) cc_final: 0.8623 (p) REVERT: C 216 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8265 (mmtt) REVERT: D 356 ILE cc_start: 0.8689 (pp) cc_final: 0.8470 (pp) REVERT: D 375 MET cc_start: 0.9115 (tpp) cc_final: 0.8817 (tpp) REVERT: D 454 GLN cc_start: 0.8123 (mt0) cc_final: 0.7919 (mt0) REVERT: E 147 ILE cc_start: 0.7763 (mt) cc_final: 0.7519 (mt) REVERT: F 292 MET cc_start: 0.5599 (ttp) cc_final: 0.5334 (ttp) REVERT: G 329 MET cc_start: 0.7438 (mmm) cc_final: 0.7019 (mmm) REVERT: G 333 PHE cc_start: 0.7257 (m-10) cc_final: 0.6891 (m-80) REVERT: H 215 TYR cc_start: 0.7679 (m-80) cc_final: 0.7435 (m-80) REVERT: H 282 TYR cc_start: 0.7488 (t80) cc_final: 0.6810 (t80) REVERT: P 277 VAL cc_start: 0.8282 (t) cc_final: 0.7943 (t) REVERT: S 42 VAL cc_start: 0.8847 (m) cc_final: 0.8614 (m) REVERT: S 68 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7707 (ttp80) REVERT: T 90 TYR cc_start: 0.4316 (t80) cc_final: 0.4099 (t80) REVERT: T 144 ILE cc_start: 0.7688 (mt) cc_final: 0.7391 (mt) REVERT: T 146 ASP cc_start: 0.7215 (m-30) cc_final: 0.7014 (m-30) REVERT: V 53 ASN cc_start: 0.7111 (m-40) cc_final: 0.6904 (m-40) REVERT: W 39 TYR cc_start: 0.8860 (t80) cc_final: 0.8653 (t80) REVERT: W 65 LYS cc_start: 0.8567 (tptt) cc_final: 0.8150 (mmtt) REVERT: W 69 MET cc_start: 0.8209 (mmt) cc_final: 0.7715 (mmm) REVERT: q 64 TYR cc_start: 0.8070 (m-80) cc_final: 0.7681 (m-10) outliers start: 9 outliers final: 0 residues processed: 1429 average time/residue: 0.2247 time to fit residues: 503.9583 Evaluate side-chains 882 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 881 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 68 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 0.0570 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 108 GLN B 166 ASN B 209 GLN C 73 GLN C 88 HIS C 123 ASN C 179 ASN C 195 HIS C 227 GLN D 117 HIS D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 HIS D 346 GLN D 381 HIS ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN F 103 ASN F 133 HIS F 168 ASN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN G 140 GLN G 164 ASN G 331 GLN G 460 HIS G 495 ASN G 569 GLN ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 97 ASN H 169 GLN H 258 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN P 71 ASN P 121 GLN P 251 ASN Q 51 GLN Q 88 GLN V 50 GLN V 110 ASN W 105 HIS W 111 HIS X 30 HIS X 40 ASN X 99 HIS X 109 GLN Z 24 ASN a 31 ASN b 69 HIS b 71 GLN q 12 GLN q 31 ASN q 54 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 GLN r 21 GLN ** r 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 59 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.159115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123745 restraints weight = 54295.872| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.27 r_work: 0.3545 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34860 Z= 0.187 Angle : 0.993 70.483 47266 Z= 0.408 Chirality : 0.049 0.239 5152 Planarity : 0.006 0.156 5985 Dihedral : 10.041 144.486 4915 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.49 % Rotamer: Outliers : 3.63 % Allowed : 14.91 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.85 (0.13), residues: 4136 helix: 0.29 (0.12), residues: 1873 sheet: -0.93 (0.26), residues: 377 loop : -1.31 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 78 TYR 0.029 0.002 TYR b 41 PHE 0.028 0.002 PHE H 223 TRP 0.020 0.002 TRP Z 116 HIS 0.013 0.002 HIS b 69 Details of bonding type rmsd covalent geometry : bond 0.00416 (34820) covalent geometry : angle 0.79109 (47176) SS BOND : bond 0.00542 ( 3) SS BOND : angle 3.43295 ( 6) hydrogen bonds : bond 0.05589 ( 1432) hydrogen bonds : angle 5.66560 ( 4152) metal coordination : bond 0.02278 ( 37) metal coordination : angle 14.21183 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 947 time to evaluate : 1.287 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: A 87 MET cc_start: 0.8727 (tmm) cc_final: 0.7343 (tmm) REVERT: B 94 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8151 (m) REVERT: B 147 LYS cc_start: 0.8726 (tptt) cc_final: 0.7984 (ttpt) REVERT: B 213 LYS cc_start: 0.9016 (tttt) cc_final: 0.8572 (ttmt) REVERT: C 238 TRP cc_start: 0.8532 (m100) cc_final: 0.7769 (m100) REVERT: E 67 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7843 (ttmm) REVERT: E 69 TYR cc_start: 0.7819 (m-80) cc_final: 0.7569 (m-80) REVERT: E 148 LEU cc_start: 0.8535 (tp) cc_final: 0.8290 (tt) REVERT: E 168 PHE cc_start: 0.8351 (m-80) cc_final: 0.7774 (m-10) REVERT: F 68 ILE cc_start: 0.8499 (mt) cc_final: 0.8299 (tp) REVERT: F 115 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8350 (p) REVERT: F 149 MET cc_start: 0.7804 (mtm) cc_final: 0.7506 (mpp) REVERT: F 450 MET cc_start: 0.8835 (mmt) cc_final: 0.8075 (mmt) REVERT: F 457 HIS cc_start: 0.7132 (m-70) cc_final: 0.6907 (m-70) REVERT: G 370 GLU cc_start: 0.7815 (tp30) cc_final: 0.7540 (mm-30) REVERT: G 380 ASP cc_start: 0.7892 (m-30) cc_final: 0.7679 (m-30) REVERT: G 513 MET cc_start: 0.7768 (tpp) cc_final: 0.7519 (tpt) REVERT: H 89 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9014 (mp) REVERT: H 92 PRO cc_start: 0.7615 (Cg_endo) cc_final: 0.7404 (Cg_endo) REVERT: H 142 TYR cc_start: 0.8425 (m-80) cc_final: 0.7244 (m-80) REVERT: H 181 MET cc_start: 0.8716 (mtt) cc_final: 0.8472 (mtt) REVERT: H 195 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.8061 (mmm160) REVERT: H 304 HIS cc_start: 0.8141 (m170) cc_final: 0.7837 (m170) REVERT: H 311 THR cc_start: 0.8715 (p) cc_final: 0.8271 (p) REVERT: I 49 ASP cc_start: 0.8585 (m-30) cc_final: 0.8097 (p0) REVERT: I 50 MET cc_start: 0.6272 (mmm) cc_final: 0.5787 (ptp) REVERT: I 149 MET cc_start: 0.8449 (mmm) cc_final: 0.8237 (mmt) REVERT: P 121 GLN cc_start: 0.8635 (mt0) cc_final: 0.8349 (mt0) REVERT: P 278 LYS cc_start: 0.8628 (pttt) cc_final: 0.8307 (ptmt) REVERT: P 283 MET cc_start: 0.8917 (mmm) cc_final: 0.8687 (mmm) REVERT: Q 123 ASN cc_start: 0.8731 (m-40) cc_final: 0.8481 (m-40) REVERT: Q 146 ASP cc_start: 0.8430 (p0) cc_final: 0.8124 (p0) REVERT: Q 148 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7853 (mt-10) REVERT: R 101 THR cc_start: 0.6699 (p) cc_final: 0.6340 (p) REVERT: S 46 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8509 (mttp) REVERT: T 84 LEU cc_start: 0.8939 (tt) cc_final: 0.8669 (mp) REVERT: T 114 ASP cc_start: 0.8190 (m-30) cc_final: 0.7700 (t70) REVERT: T 117 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7908 (mp0) REVERT: V 32 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8684 (mp) REVERT: V 53 ASN cc_start: 0.7887 (m-40) cc_final: 0.7535 (m110) REVERT: W 29 ASN cc_start: 0.8954 (m-40) cc_final: 0.8728 (m-40) REVERT: W 69 MET cc_start: 0.8831 (mmt) cc_final: 0.8379 (mmm) REVERT: W 71 MET cc_start: 0.8761 (tpp) cc_final: 0.8327 (mmt) REVERT: X 50 GLU cc_start: 0.8527 (tp30) cc_final: 0.8258 (mp0) REVERT: X 134 ASP cc_start: 0.8232 (p0) cc_final: 0.7719 (m-30) REVERT: Z 24 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7924 (t0) REVERT: Z 72 MET cc_start: 0.9019 (ttp) cc_final: 0.8789 (ttp) REVERT: Z 116 TRP cc_start: 0.8518 (t-100) cc_final: 0.8105 (t-100) REVERT: b 8 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6760 (p90) REVERT: b 10 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8170 (tptt) REVERT: s 48 LEU cc_start: 0.7464 (tp) cc_final: 0.7221 (tt) outliers start: 132 outliers final: 57 residues processed: 1021 average time/residue: 0.2156 time to fit residues: 353.9942 Evaluate side-chains 840 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 775 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 405 ARG Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain P residue 315 THR Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 24 ASN Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 90 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 294 optimal weight: 0.0980 chunk 376 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 227 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 265 ASN E 86 GLN E 152 GLN F 103 ASN F 133 HIS ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN G 260 ASN G 444 HIS G 571 HIS G 604 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN I 159 GLN P 216 HIS P 323 HIS P 341 GLN V 21 HIS X 64 ASN X 95 GLN Z 24 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN b 69 HIS q 12 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 135 HIS r 110 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.158523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.122818 restraints weight = 54459.160| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.40 r_work: 0.3525 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 34860 Z= 0.157 Angle : 0.879 71.251 47266 Z= 0.350 Chirality : 0.045 0.296 5152 Planarity : 0.005 0.139 5985 Dihedral : 9.450 133.763 4911 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 3.63 % Allowed : 17.08 % Favored : 79.28 % 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: 4136 helix: 0.65 (0.12), residues: 1883 sheet: -0.97 (0.27), residues: 366 loop : -1.08 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 135 TYR 0.020 0.002 TYR E 129 PHE 0.023 0.002 PHE T 126 TRP 0.019 0.001 TRP E 91 HIS 0.007 0.001 HIS b 69 Details of bonding type rmsd covalent geometry : bond 0.00361 (34820) covalent geometry : angle 0.68551 (47176) SS BOND : bond 0.00830 ( 3) SS BOND : angle 3.63349 ( 6) hydrogen bonds : bond 0.04827 ( 1432) hydrogen bonds : angle 5.24408 ( 4152) metal coordination : bond 0.01968 ( 37) metal coordination : angle 13.05107 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 822 time to evaluate : 1.274 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: B 147 LYS cc_start: 0.8891 (tptt) cc_final: 0.8167 (ttpt) REVERT: B 213 LYS cc_start: 0.8994 (tttt) cc_final: 0.8597 (ttmt) REVERT: B 223 ARG cc_start: 0.8000 (mtt-85) cc_final: 0.7578 (mpt-90) REVERT: D 266 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8114 (ttm110) REVERT: E 129 TYR cc_start: 0.7571 (m-10) cc_final: 0.6682 (m-10) REVERT: E 148 LEU cc_start: 0.8539 (tp) cc_final: 0.8328 (tt) REVERT: E 168 PHE cc_start: 0.8363 (m-80) cc_final: 0.7979 (m-10) REVERT: E 186 GLN cc_start: 0.7188 (tt0) cc_final: 0.6960 (tt0) REVERT: E 207 LEU cc_start: 0.7870 (mt) cc_final: 0.7327 (mt) REVERT: F 103 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.8013 (t0) REVERT: F 450 MET cc_start: 0.8904 (mmt) cc_final: 0.8116 (mmt) REVERT: G 315 THR cc_start: 0.8658 (m) cc_final: 0.8424 (p) REVERT: G 316 TYR cc_start: 0.8290 (m-80) cc_final: 0.8070 (m-80) REVERT: G 325 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7647 (mtt-85) REVERT: G 329 MET cc_start: 0.8359 (mmm) cc_final: 0.8157 (mmm) REVERT: G 370 GLU cc_start: 0.7888 (tp30) cc_final: 0.7624 (mm-30) REVERT: G 380 ASP cc_start: 0.7998 (m-30) cc_final: 0.7731 (m-30) REVERT: H 89 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9012 (mp) REVERT: H 92 PRO cc_start: 0.7764 (Cg_exo) cc_final: 0.7523 (Cg_endo) REVERT: H 142 TYR cc_start: 0.8527 (m-80) cc_final: 0.7462 (m-80) REVERT: H 181 MET cc_start: 0.8698 (mtt) cc_final: 0.8385 (mtt) REVERT: H 183 MET cc_start: 0.8973 (mtt) cc_final: 0.8755 (mtp) REVERT: H 195 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.8014 (mmm160) REVERT: H 215 TYR cc_start: 0.8475 (m-80) cc_final: 0.8214 (m-80) REVERT: H 304 HIS cc_start: 0.8118 (m170) cc_final: 0.7841 (m170) REVERT: I 49 ASP cc_start: 0.8499 (m-30) cc_final: 0.8295 (p0) REVERT: I 50 MET cc_start: 0.6128 (mmm) cc_final: 0.5592 (ptm) REVERT: I 62 MET cc_start: 0.8874 (mtt) cc_final: 0.8654 (mtt) REVERT: P 52 SER cc_start: 0.7805 (OUTLIER) cc_final: 0.7524 (p) REVERT: P 121 GLN cc_start: 0.8790 (mt0) cc_final: 0.8511 (mt0) REVERT: P 278 LYS cc_start: 0.8555 (pttt) cc_final: 0.8131 (ptmt) REVERT: P 311 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7232 (pm20) REVERT: P 354 ARG cc_start: 0.8049 (tpp-160) cc_final: 0.7846 (mtt-85) REVERT: Q 94 THR cc_start: 0.9012 (m) cc_final: 0.8768 (p) REVERT: Q 123 ASN cc_start: 0.8707 (m-40) cc_final: 0.8436 (m-40) REVERT: Q 146 ASP cc_start: 0.8403 (p0) cc_final: 0.8186 (p0) REVERT: Q 148 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7856 (mt-10) REVERT: S 44 LEU cc_start: 0.8992 (mt) cc_final: 0.8524 (mp) REVERT: T 84 LEU cc_start: 0.8838 (tt) cc_final: 0.8619 (mp) REVERT: T 114 ASP cc_start: 0.8164 (m-30) cc_final: 0.7769 (t70) REVERT: T 117 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7888 (mp0) REVERT: T 142 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: V 32 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8540 (mp) REVERT: V 67 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8039 (ttmm) REVERT: V 94 MET cc_start: 0.8050 (mmm) cc_final: 0.7638 (mtp) REVERT: W 29 ASN cc_start: 0.8961 (m-40) cc_final: 0.8706 (m-40) REVERT: W 37 GLU cc_start: 0.8926 (tp30) cc_final: 0.8648 (tp30) REVERT: W 68 GLU cc_start: 0.8718 (tt0) cc_final: 0.8345 (tt0) REVERT: W 69 MET cc_start: 0.8744 (mmt) cc_final: 0.8343 (mmm) REVERT: W 71 MET cc_start: 0.8681 (tpp) cc_final: 0.8455 (mmt) REVERT: W 107 MET cc_start: 0.8344 (mmt) cc_final: 0.8066 (mmt) REVERT: X 16 GLU cc_start: 0.7664 (tp30) cc_final: 0.7338 (tm-30) REVERT: X 50 GLU cc_start: 0.8427 (tp30) cc_final: 0.8187 (mp0) REVERT: X 56 CYS cc_start: 0.5701 (OUTLIER) cc_final: 0.5398 (p) REVERT: X 59 GLU cc_start: 0.7981 (mp0) cc_final: 0.7219 (mp0) REVERT: X 124 GLN cc_start: 0.7672 (mt0) cc_final: 0.7423 (pt0) REVERT: Z 97 ILE cc_start: 0.6796 (mm) cc_final: 0.6525 (mm) REVERT: b 8 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6707 (p90) REVERT: b 10 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8172 (tptm) REVERT: b 82 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7799 (mtmt) REVERT: r 93 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7889 (mmmm) outliers start: 132 outliers final: 72 residues processed: 890 average time/residue: 0.2050 time to fit residues: 296.2887 Evaluate side-chains 818 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 739 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 315 THR Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 347 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 142 GLN Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 85 GLU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 74 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 313 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 250 optimal weight: 0.5980 chunk 384 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 HIS C 227 GLN D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN E 86 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 HIS V 21 HIS V 50 GLN Z 112 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN q 59 HIS q 87 HIS q 91 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.154690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.115143 restraints weight = 54647.432| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.30 r_work: 0.3377 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 34860 Z= 0.200 Angle : 0.882 73.917 47266 Z= 0.346 Chirality : 0.046 0.318 5152 Planarity : 0.005 0.137 5985 Dihedral : 9.296 136.241 4911 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 4.26 % Allowed : 17.77 % 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: -0.32 (0.13), residues: 4136 helix: 0.72 (0.12), residues: 1870 sheet: -0.90 (0.26), residues: 391 loop : -0.97 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 59 TYR 0.020 0.002 TYR D 385 PHE 0.018 0.002 PHE D 174 TRP 0.020 0.001 TRP E 91 HIS 0.006 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00474 (34820) covalent geometry : angle 0.68090 (47176) SS BOND : bond 0.03207 ( 3) SS BOND : angle 3.47185 ( 6) hydrogen bonds : bond 0.04550 ( 1432) hydrogen bonds : angle 5.10483 ( 4152) metal coordination : bond 0.02384 ( 37) metal coordination : angle 13.27641 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 780 time to evaluate : 1.220 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 65 PHE cc_start: 0.9205 (m-80) cc_final: 0.8865 (m-80) REVERT: A 108 GLN cc_start: 0.8397 (tp40) cc_final: 0.8191 (tp-100) REVERT: B 147 LYS cc_start: 0.8840 (tptt) cc_final: 0.8151 (ttpt) REVERT: B 213 LYS cc_start: 0.9030 (tttt) cc_final: 0.8739 (ttpt) REVERT: B 223 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7601 (mpt-90) REVERT: C 171 ASP cc_start: 0.8610 (t0) cc_final: 0.8400 (t0) REVERT: D 266 ARG cc_start: 0.8753 (ttm110) cc_final: 0.8462 (ttm-80) REVERT: E 65 ILE cc_start: 0.8628 (mp) cc_final: 0.8216 (mp) REVERT: E 129 TYR cc_start: 0.7534 (m-10) cc_final: 0.7006 (m-10) REVERT: E 150 THR cc_start: 0.7855 (m) cc_final: 0.7384 (p) REVERT: F 80 MET cc_start: 0.8625 (mmp) cc_final: 0.8199 (mmm) REVERT: F 337 MET cc_start: 0.7752 (mtp) cc_final: 0.7523 (ttm) REVERT: F 355 ILE cc_start: 0.7915 (mt) cc_final: 0.7619 (mt) REVERT: F 450 MET cc_start: 0.8934 (mmt) cc_final: 0.8081 (mmt) REVERT: G 315 THR cc_start: 0.8681 (m) cc_final: 0.8420 (p) REVERT: G 316 TYR cc_start: 0.8501 (m-80) cc_final: 0.8239 (m-80) REVERT: G 329 MET cc_start: 0.8444 (mmm) cc_final: 0.7720 (mmp) REVERT: G 333 PHE cc_start: 0.7985 (m-10) cc_final: 0.6964 (m-80) REVERT: G 380 ASP cc_start: 0.8175 (m-30) cc_final: 0.7842 (m-30) REVERT: G 510 TRP cc_start: 0.8265 (t-100) cc_final: 0.7988 (t-100) REVERT: G 538 ARG cc_start: 0.7416 (mtp85) cc_final: 0.7205 (mtp85) REVERT: H 89 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9108 (mp) REVERT: H 92 PRO cc_start: 0.8136 (Cg_exo) cc_final: 0.7923 (Cg_endo) REVERT: H 142 TYR cc_start: 0.8828 (m-80) cc_final: 0.7796 (m-80) REVERT: H 173 TRP cc_start: 0.8338 (m-10) cc_final: 0.8107 (m-10) REVERT: H 195 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8132 (mmm160) REVERT: H 215 TYR cc_start: 0.8485 (m-80) cc_final: 0.8281 (m-80) REVERT: H 261 MET cc_start: 0.8723 (mmm) cc_final: 0.8496 (mmm) REVERT: H 277 TYR cc_start: 0.8629 (m-80) cc_final: 0.8200 (m-80) REVERT: I 49 ASP cc_start: 0.8443 (m-30) cc_final: 0.8196 (p0) REVERT: I 50 MET cc_start: 0.6200 (mmm) cc_final: 0.5743 (ptm) REVERT: I 62 MET cc_start: 0.9022 (mtt) cc_final: 0.8743 (mtt) REVERT: I 208 ASP cc_start: 0.8441 (t0) cc_final: 0.7896 (t70) REVERT: P 43 HIS cc_start: 0.7652 (m90) cc_final: 0.7304 (m90) REVERT: P 102 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6150 (mm-40) REVERT: P 121 GLN cc_start: 0.8900 (mt0) cc_final: 0.8557 (mt0) REVERT: P 311 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7100 (pm20) REVERT: P 354 ARG cc_start: 0.8159 (tpp-160) cc_final: 0.7953 (mtt-85) REVERT: Q 146 ASP cc_start: 0.8530 (p0) cc_final: 0.8313 (p0) REVERT: Q 148 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7917 (mt-10) REVERT: Q 156 LYS cc_start: 0.8149 (mttp) cc_final: 0.7486 (mtpp) REVERT: S 17 ARG cc_start: 0.8357 (mmm160) cc_final: 0.7993 (mmp80) REVERT: S 31 GLN cc_start: 0.7831 (tp40) cc_final: 0.7543 (tp-100) REVERT: S 62 GLN cc_start: 0.8407 (pm20) cc_final: 0.8162 (pm20) REVERT: T 84 LEU cc_start: 0.8883 (tt) cc_final: 0.8656 (mp) REVERT: T 114 ASP cc_start: 0.8199 (m-30) cc_final: 0.7548 (m-30) REVERT: T 117 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7878 (mp0) REVERT: V 29 THR cc_start: 0.8813 (t) cc_final: 0.8583 (p) REVERT: V 32 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8534 (mp) REVERT: V 67 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8142 (ttmm) REVERT: V 81 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8668 (mp) REVERT: W 58 THR cc_start: 0.8561 (m) cc_final: 0.8202 (p) REVERT: W 68 GLU cc_start: 0.8922 (tt0) cc_final: 0.8654 (tt0) REVERT: W 69 MET cc_start: 0.8848 (mmt) cc_final: 0.8344 (mmm) REVERT: W 107 MET cc_start: 0.8342 (mmt) cc_final: 0.7976 (mmt) REVERT: W 119 LYS cc_start: 0.8659 (mttt) cc_final: 0.8434 (mmtm) REVERT: X 16 GLU cc_start: 0.7675 (tp30) cc_final: 0.7344 (tm-30) REVERT: X 124 GLN cc_start: 0.7870 (mt0) cc_final: 0.7399 (pt0) REVERT: Z 24 ASN cc_start: 0.8366 (t0) cc_final: 0.8137 (t0) REVERT: Z 86 ILE cc_start: 0.8998 (mm) cc_final: 0.8762 (mt) REVERT: Z 97 ILE cc_start: 0.7117 (mm) cc_final: 0.6835 (mm) REVERT: b 8 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.6535 (p90) REVERT: b 10 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8191 (tptt) REVERT: b 82 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7939 (mtmt) outliers start: 155 outliers final: 92 residues processed: 872 average time/residue: 0.2011 time to fit residues: 285.4430 Evaluate side-chains 802 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 705 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 405 ARG Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 102 GLN Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 315 THR Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 142 GLN Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 368 optimal weight: 1.9990 chunk 400 optimal weight: 0.4980 chunk 237 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 249 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 HIS D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN E 86 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN G 205 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 ASN R 33 HIS V 21 HIS V 50 GLN W 73 ASN b 11 ASN b 52 ASN b 69 HIS q 72 ASN r 110 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.118152 restraints weight = 54985.136| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.29 r_work: 0.3412 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 34860 Z= 0.137 Angle : 0.834 74.813 47266 Z= 0.321 Chirality : 0.043 0.335 5152 Planarity : 0.005 0.134 5985 Dihedral : 9.025 132.419 4911 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Rotamer: Outliers : 3.85 % Allowed : 19.01 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.18 (0.13), residues: 4136 helix: 0.86 (0.12), residues: 1879 sheet: -0.93 (0.26), residues: 387 loop : -0.91 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 323 TYR 0.016 0.001 TYR D 286 PHE 0.023 0.001 PHE E 168 TRP 0.016 0.001 TRP A 106 HIS 0.009 0.001 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00320 (34820) covalent geometry : angle 0.63361 (47176) SS BOND : bond 0.00605 ( 3) SS BOND : angle 3.11172 ( 6) hydrogen bonds : bond 0.04140 ( 1432) hydrogen bonds : angle 4.92490 ( 4152) metal coordination : bond 0.01519 ( 37) metal coordination : angle 12.84903 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 762 time to evaluate : 1.360 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 65 PHE cc_start: 0.9155 (m-80) cc_final: 0.8917 (m-80) REVERT: A 108 GLN cc_start: 0.8439 (tp40) cc_final: 0.8238 (tp-100) REVERT: B 147 LYS cc_start: 0.8823 (tptt) cc_final: 0.8113 (ttpt) REVERT: B 213 LYS cc_start: 0.9001 (tttt) cc_final: 0.8708 (ttpt) REVERT: B 223 ARG cc_start: 0.7972 (mtt-85) cc_final: 0.7599 (mpt-90) REVERT: C 171 ASP cc_start: 0.8536 (t0) cc_final: 0.8263 (t0) REVERT: C 227 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: D 266 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8458 (ttm-80) REVERT: E 150 THR cc_start: 0.7788 (m) cc_final: 0.7377 (p) REVERT: E 204 ILE cc_start: 0.8749 (mm) cc_final: 0.8528 (mt) REVERT: F 80 MET cc_start: 0.8669 (mmp) cc_final: 0.8179 (mmm) REVERT: F 405 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8293 (mmt180) REVERT: F 450 MET cc_start: 0.8959 (mmt) cc_final: 0.8118 (mmt) REVERT: G 173 MET cc_start: 0.9025 (tpp) cc_final: 0.8795 (tpp) REVERT: G 315 THR cc_start: 0.8679 (m) cc_final: 0.8452 (p) REVERT: G 316 TYR cc_start: 0.8611 (m-80) cc_final: 0.8208 (m-80) REVERT: G 510 TRP cc_start: 0.8250 (t-100) cc_final: 0.7945 (t-100) REVERT: H 89 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9055 (mp) REVERT: H 92 PRO cc_start: 0.8135 (Cg_exo) cc_final: 0.7890 (Cg_endo) REVERT: H 142 TYR cc_start: 0.8809 (m-80) cc_final: 0.7872 (m-80) REVERT: H 173 TRP cc_start: 0.8330 (m-10) cc_final: 0.8118 (m-10) REVERT: H 277 TYR cc_start: 0.8594 (m-80) cc_final: 0.8188 (m-80) REVERT: I 49 ASP cc_start: 0.8431 (m-30) cc_final: 0.8187 (p0) REVERT: I 50 MET cc_start: 0.5917 (mmm) cc_final: 0.5580 (ptm) REVERT: I 62 MET cc_start: 0.8983 (mtt) cc_final: 0.8759 (mtt) REVERT: I 208 ASP cc_start: 0.8479 (t0) cc_final: 0.7952 (t70) REVERT: P 121 GLN cc_start: 0.8920 (mt0) cc_final: 0.8585 (mt0) REVERT: P 254 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8265 (ttmt) REVERT: P 311 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7052 (pm20) REVERT: P 354 ARG cc_start: 0.8157 (tpp-160) cc_final: 0.7889 (mtt-85) REVERT: Q 146 ASP cc_start: 0.8530 (p0) cc_final: 0.8248 (p0) REVERT: Q 148 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7944 (mt-10) REVERT: Q 164 PHE cc_start: 0.8626 (m-10) cc_final: 0.8407 (m-10) REVERT: S 31 GLN cc_start: 0.7902 (tp40) cc_final: 0.7667 (tp-100) REVERT: T 82 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7938 (mtt90) REVERT: T 84 LEU cc_start: 0.8901 (tt) cc_final: 0.8683 (mp) REVERT: T 114 ASP cc_start: 0.8320 (m-30) cc_final: 0.7656 (m-30) REVERT: T 117 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7819 (mp0) REVERT: T 132 ASP cc_start: 0.7733 (m-30) cc_final: 0.6629 (m-30) REVERT: V 67 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8157 (ttmm) REVERT: V 81 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8614 (mp) REVERT: W 37 GLU cc_start: 0.8934 (tp30) cc_final: 0.8363 (mm-30) REVERT: W 58 THR cc_start: 0.8555 (m) cc_final: 0.8269 (p) REVERT: W 68 GLU cc_start: 0.8941 (tt0) cc_final: 0.8741 (tt0) REVERT: W 107 MET cc_start: 0.8415 (mmt) cc_final: 0.7973 (mmt) REVERT: X 124 GLN cc_start: 0.7616 (mt0) cc_final: 0.7282 (pt0) REVERT: Z 24 ASN cc_start: 0.8408 (t0) cc_final: 0.8179 (t0) REVERT: Z 123 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7499 (pt0) REVERT: b 8 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.6259 (p90) REVERT: b 10 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8178 (tptt) REVERT: b 32 MET cc_start: 0.8638 (mmt) cc_final: 0.8247 (mmt) REVERT: r 11 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6320 (tt) REVERT: r 92 LYS cc_start: 0.7682 (tmtt) cc_final: 0.7455 (tptm) outliers start: 140 outliers final: 91 residues processed: 842 average time/residue: 0.2057 time to fit residues: 280.8596 Evaluate side-chains 793 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 696 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 405 ARG Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 566 ILE 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 659 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 315 THR Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 142 GLN Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 116 TRP Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 85 GLU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 322 optimal weight: 0.0270 chunk 107 optimal weight: 5.9990 chunk 8 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 335 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS G 51 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 ASN Q 123 ASN V 21 HIS V 50 GLN V 83 GLN W 73 ASN ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.157741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.118960 restraints weight = 55076.496| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.30 r_work: 0.3423 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 34860 Z= 0.128 Angle : 0.824 75.390 47266 Z= 0.315 Chirality : 0.043 0.315 5152 Planarity : 0.005 0.132 5985 Dihedral : 8.868 133.019 4911 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.81 % Rotamer: Outliers : 3.49 % Allowed : 20.19 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: 4136 helix: 0.94 (0.12), residues: 1869 sheet: -0.91 (0.26), residues: 377 loop : -0.84 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 323 TYR 0.019 0.001 TYR V 44 PHE 0.023 0.001 PHE H 211 TRP 0.017 0.001 TRP A 106 HIS 0.007 0.001 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00299 (34820) covalent geometry : angle 0.62567 (47176) SS BOND : bond 0.00585 ( 3) SS BOND : angle 2.62260 ( 6) hydrogen bonds : bond 0.03956 ( 1432) hydrogen bonds : angle 4.89696 ( 4152) metal coordination : bond 0.01364 ( 37) metal coordination : angle 12.71215 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 740 time to evaluate : 1.268 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 49 LEU cc_start: 0.7197 (tt) cc_final: 0.6978 (tp) REVERT: A 108 GLN cc_start: 0.8410 (tp40) cc_final: 0.8195 (tp-100) REVERT: B 147 LYS cc_start: 0.8790 (tptt) cc_final: 0.8167 (ttpt) REVERT: B 213 LYS cc_start: 0.8985 (tttt) cc_final: 0.8663 (ttpt) REVERT: B 223 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7592 (mpt-90) REVERT: C 171 ASP cc_start: 0.8501 (t0) cc_final: 0.8226 (t0) REVERT: D 263 THR cc_start: 0.8561 (t) cc_final: 0.8311 (m) REVERT: D 335 GLU cc_start: 0.8176 (tp30) cc_final: 0.7924 (tp30) REVERT: E 150 THR cc_start: 0.7747 (m) cc_final: 0.7291 (p) REVERT: E 155 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8386 (mm) REVERT: F 80 MET cc_start: 0.8691 (mmp) cc_final: 0.8251 (mmm) REVERT: F 100 SER cc_start: 0.8263 (t) cc_final: 0.7938 (p) REVERT: F 149 MET cc_start: 0.7790 (mtm) cc_final: 0.7373 (mpp) REVERT: F 405 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8331 (mmt180) REVERT: F 450 MET cc_start: 0.8985 (mmt) cc_final: 0.8305 (mmt) REVERT: G 150 ARG cc_start: 0.7594 (mtt-85) cc_final: 0.6903 (mtt-85) REVERT: G 173 MET cc_start: 0.9008 (tpp) cc_final: 0.8805 (tpp) REVERT: G 315 THR cc_start: 0.8702 (m) cc_final: 0.8492 (p) REVERT: G 316 TYR cc_start: 0.8564 (m-80) cc_final: 0.8177 (m-80) REVERT: G 423 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8836 (mp) REVERT: G 510 TRP cc_start: 0.8300 (t-100) cc_final: 0.7983 (t-100) REVERT: G 513 MET cc_start: 0.8123 (tpp) cc_final: 0.7703 (tpt) REVERT: H 17 MET cc_start: 0.9104 (tmm) cc_final: 0.8772 (tmm) REVERT: H 92 PRO cc_start: 0.8120 (Cg_exo) cc_final: 0.7855 (Cg_endo) REVERT: H 142 TYR cc_start: 0.8767 (m-80) cc_final: 0.7882 (m-80) REVERT: H 215 TYR cc_start: 0.8441 (m-80) cc_final: 0.8083 (m-80) REVERT: H 277 TYR cc_start: 0.8592 (m-80) cc_final: 0.8276 (m-80) REVERT: I 49 ASP cc_start: 0.8389 (m-30) cc_final: 0.8131 (p0) REVERT: I 50 MET cc_start: 0.5968 (mmm) cc_final: 0.5599 (ptm) REVERT: I 89 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: I 208 ASP cc_start: 0.8445 (t0) cc_final: 0.7906 (t70) REVERT: P 254 LYS cc_start: 0.8482 (ttpt) cc_final: 0.8180 (ttmt) REVERT: P 310 PHE cc_start: 0.5380 (OUTLIER) cc_final: 0.4394 (m-80) REVERT: P 311 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7025 (pm20) REVERT: P 354 ARG cc_start: 0.8154 (tpp-160) cc_final: 0.7882 (mtt-85) REVERT: Q 146 ASP cc_start: 0.8505 (p0) cc_final: 0.8226 (p0) REVERT: S 17 ARG cc_start: 0.8348 (mmm160) cc_final: 0.8038 (mmp80) REVERT: S 31 GLN cc_start: 0.7869 (tp40) cc_final: 0.7611 (tp-100) REVERT: T 84 LEU cc_start: 0.8879 (tt) cc_final: 0.8674 (mp) REVERT: T 114 ASP cc_start: 0.8290 (m-30) cc_final: 0.7721 (m-30) REVERT: T 117 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7796 (mt-10) REVERT: V 67 LYS cc_start: 0.8626 (mmtp) cc_final: 0.7942 (ttmm) REVERT: V 81 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8619 (mp) REVERT: W 37 GLU cc_start: 0.8950 (tp30) cc_final: 0.8361 (mm-30) REVERT: W 58 THR cc_start: 0.8569 (m) cc_final: 0.8315 (p) REVERT: W 68 GLU cc_start: 0.8884 (tt0) cc_final: 0.8669 (tt0) REVERT: X 124 GLN cc_start: 0.7658 (mt0) cc_final: 0.7430 (pt0) REVERT: X 132 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8346 (tptt) REVERT: Z 24 ASN cc_start: 0.8386 (t0) cc_final: 0.8100 (t0) REVERT: Z 50 MET cc_start: 0.8611 (tpp) cc_final: 0.8281 (tpp) REVERT: Z 123 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7449 (pt0) REVERT: a 1 MET cc_start: 0.5462 (mmt) cc_final: 0.5056 (mtt) REVERT: b 10 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8207 (tptt) REVERT: b 32 MET cc_start: 0.8619 (mmt) cc_final: 0.8364 (mmm) REVERT: q 81 MET cc_start: 0.7373 (mtm) cc_final: 0.7049 (mtm) REVERT: r 101 MET cc_start: 0.8780 (ttp) cc_final: 0.8532 (ttt) outliers start: 127 outliers final: 90 residues processed: 816 average time/residue: 0.2089 time to fit residues: 275.4238 Evaluate side-chains 791 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 695 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 405 ARG Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 566 ILE 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 659 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 310 PHE Chi-restraints excluded: chain P residue 315 THR Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 142 GLN Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 116 TRP Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 85 GLU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 215 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 338 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 349 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN F 44 ASN G 202 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN P 219 ASN Q 123 ASN V 21 HIS b 11 ASN b 52 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.154218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.117221 restraints weight = 54800.602| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.54 r_work: 0.3377 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 34860 Z= 0.152 Angle : 0.835 75.617 47266 Z= 0.321 Chirality : 0.043 0.286 5152 Planarity : 0.005 0.133 5985 Dihedral : 8.759 133.108 4911 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 3.44 % Allowed : 19.94 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.05 (0.13), residues: 4136 helix: 0.97 (0.12), residues: 1878 sheet: -0.89 (0.26), residues: 385 loop : -0.82 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 72 TYR 0.028 0.002 TYR b 53 PHE 0.030 0.002 PHE A 51 TRP 0.020 0.001 TRP F 99 HIS 0.034 0.001 HIS F 303 Details of bonding type rmsd covalent geometry : bond 0.00361 (34820) covalent geometry : angle 0.63925 (47176) SS BOND : bond 0.01095 ( 3) SS BOND : angle 2.39139 ( 6) hydrogen bonds : bond 0.04013 ( 1432) hydrogen bonds : angle 4.88289 ( 4152) metal coordination : bond 0.01803 ( 37) metal coordination : angle 12.74982 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 744 time to evaluate : 1.198 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: A 2 ASN cc_start: 0.8142 (m-40) cc_final: 0.7765 (m-40) REVERT: A 108 GLN cc_start: 0.8356 (tp40) cc_final: 0.8151 (tp-100) REVERT: B 147 LYS cc_start: 0.8628 (tptt) cc_final: 0.8092 (ttpt) REVERT: B 152 MET cc_start: 0.8169 (mtt) cc_final: 0.7965 (mtt) REVERT: B 213 LYS cc_start: 0.8979 (tttt) cc_final: 0.8656 (ttpt) REVERT: B 223 ARG cc_start: 0.7995 (mtt-85) cc_final: 0.7636 (mpt-90) REVERT: C 171 ASP cc_start: 0.8394 (t0) cc_final: 0.8131 (t0) REVERT: E 61 ARG cc_start: 0.7475 (mtt90) cc_final: 0.7206 (mtm-85) REVERT: E 91 TRP cc_start: 0.6572 (t-100) cc_final: 0.6232 (t-100) REVERT: E 150 THR cc_start: 0.7703 (m) cc_final: 0.7285 (p) REVERT: E 155 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8409 (mm) REVERT: F 80 MET cc_start: 0.8715 (mmp) cc_final: 0.8245 (mmm) REVERT: F 100 SER cc_start: 0.8276 (t) cc_final: 0.7939 (p) REVERT: F 149 MET cc_start: 0.7808 (mtm) cc_final: 0.7434 (mpp) REVERT: F 405 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8325 (mmt180) REVERT: F 450 MET cc_start: 0.8947 (mmt) cc_final: 0.8282 (mmt) REVERT: G 173 MET cc_start: 0.8981 (tpp) cc_final: 0.8725 (tpp) REVERT: G 316 TYR cc_start: 0.8560 (m-80) cc_final: 0.8191 (m-80) REVERT: G 329 MET cc_start: 0.8292 (mmm) cc_final: 0.7558 (tpp) REVERT: G 332 ASN cc_start: 0.8385 (t0) cc_final: 0.7927 (m-40) REVERT: G 333 PHE cc_start: 0.7747 (m-10) cc_final: 0.6933 (m-80) REVERT: G 423 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8905 (mp) REVERT: G 510 TRP cc_start: 0.8351 (t-100) cc_final: 0.7999 (t-100) REVERT: G 513 MET cc_start: 0.8236 (tpp) cc_final: 0.7883 (tpt) REVERT: H 17 MET cc_start: 0.9086 (tmm) cc_final: 0.8659 (tmm) REVERT: H 92 PRO cc_start: 0.8066 (Cg_exo) cc_final: 0.7798 (Cg_endo) REVERT: H 183 MET cc_start: 0.8810 (mtt) cc_final: 0.8566 (mtp) REVERT: H 215 TYR cc_start: 0.8335 (m-80) cc_final: 0.8015 (m-80) REVERT: H 258 ASN cc_start: 0.7716 (m110) cc_final: 0.7227 (m-40) REVERT: H 261 MET cc_start: 0.8702 (mmm) cc_final: 0.8413 (mmt) REVERT: H 271 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8663 (mt) REVERT: H 277 TYR cc_start: 0.8514 (m-80) cc_final: 0.8193 (m-80) REVERT: I 41 LYS cc_start: 0.8656 (tppt) cc_final: 0.8394 (tppt) REVERT: I 49 ASP cc_start: 0.8324 (m-30) cc_final: 0.8078 (p0) REVERT: I 50 MET cc_start: 0.6044 (mmm) cc_final: 0.5614 (mmm) REVERT: I 89 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: I 94 SER cc_start: 0.9063 (p) cc_final: 0.8687 (p) REVERT: I 208 ASP cc_start: 0.8399 (t0) cc_final: 0.7930 (t70) REVERT: P 121 GLN cc_start: 0.8947 (mt0) cc_final: 0.8701 (mt0) REVERT: P 213 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7414 (t80) REVERT: P 254 LYS cc_start: 0.8495 (ttpt) cc_final: 0.8206 (ttmt) REVERT: P 311 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7005 (pm20) REVERT: P 340 VAL cc_start: 0.8072 (p) cc_final: 0.7725 (p) REVERT: Q 164 PHE cc_start: 0.8680 (m-10) cc_final: 0.8343 (m-10) REVERT: S 31 GLN cc_start: 0.7949 (tp40) cc_final: 0.7680 (tp-100) REVERT: T 93 ILE cc_start: 0.7286 (mm) cc_final: 0.7078 (pt) REVERT: T 114 ASP cc_start: 0.8230 (m-30) cc_final: 0.7661 (t70) REVERT: T 117 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7867 (mp0) REVERT: V 67 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8123 (ttmm) REVERT: V 81 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8567 (mp) REVERT: W 58 THR cc_start: 0.8577 (m) cc_final: 0.8349 (p) REVERT: Z 24 ASN cc_start: 0.8307 (t0) cc_final: 0.8072 (t0) REVERT: Z 33 TYR cc_start: 0.7584 (m-80) cc_final: 0.7366 (m-10) REVERT: Z 94 GLU cc_start: 0.7867 (tt0) cc_final: 0.7650 (pt0) REVERT: Z 97 ILE cc_start: 0.7031 (mt) cc_final: 0.6795 (mt) REVERT: a 1 MET cc_start: 0.5354 (mmt) cc_final: 0.4906 (mtt) REVERT: b 10 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8064 (mttm) REVERT: b 32 MET cc_start: 0.8556 (mmt) cc_final: 0.8337 (mmm) REVERT: q 60 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.7454 (mtp85) REVERT: r 11 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6429 (tt) REVERT: r 101 MET cc_start: 0.8712 (ttp) cc_final: 0.8496 (ttt) outliers start: 125 outliers final: 95 residues processed: 818 average time/residue: 0.1964 time to fit residues: 262.7671 Evaluate side-chains 804 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 701 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 405 ARG Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 429 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 566 ILE 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 659 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 315 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 142 GLN Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 64 ASN Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 116 TRP Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 85 GLU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 214 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 332 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 370 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 322 optimal weight: 0.0020 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN F 44 ASN F 116 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 GLN S 73 GLN V 21 HIS V 110 ASN X 124 GLN Z 85 GLN b 11 ASN b 52 ASN b 69 HIS ** r 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.154459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.117749 restraints weight = 54664.398| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.56 r_work: 0.3460 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 34860 Z= 0.148 Angle : 0.833 75.378 47266 Z= 0.320 Chirality : 0.043 0.282 5152 Planarity : 0.005 0.132 5985 Dihedral : 8.695 132.345 4911 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 3.44 % Allowed : 20.50 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.01 (0.13), residues: 4136 helix: 1.01 (0.12), residues: 1866 sheet: -0.88 (0.26), residues: 379 loop : -0.80 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 135 TYR 0.025 0.001 TYR b 53 PHE 0.026 0.001 PHE E 52 TRP 0.018 0.001 TRP A 106 HIS 0.006 0.001 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00348 (34820) covalent geometry : angle 0.63717 (47176) SS BOND : bond 0.01279 ( 3) SS BOND : angle 1.94974 ( 6) hydrogen bonds : bond 0.03945 ( 1432) hydrogen bonds : angle 4.85216 ( 4152) metal coordination : bond 0.01740 ( 37) metal coordination : angle 12.74435 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 732 time to evaluate : 1.013 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: A 2 ASN cc_start: 0.8285 (m-40) cc_final: 0.7906 (m-40) REVERT: A 108 GLN cc_start: 0.8471 (tp40) cc_final: 0.8270 (tp-100) REVERT: B 147 LYS cc_start: 0.8749 (tptt) cc_final: 0.8259 (ttpt) REVERT: B 213 LYS cc_start: 0.9092 (tttt) cc_final: 0.8798 (ttpt) REVERT: B 223 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7696 (mpt-90) REVERT: C 171 ASP cc_start: 0.8456 (t0) cc_final: 0.8175 (t0) REVERT: E 61 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7284 (mtm-85) REVERT: E 91 TRP cc_start: 0.6600 (t-100) cc_final: 0.6276 (t-100) REVERT: E 150 THR cc_start: 0.7709 (m) cc_final: 0.7293 (p) REVERT: E 155 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8419 (mm) REVERT: F 80 MET cc_start: 0.8738 (mmp) cc_final: 0.8358 (mmm) REVERT: F 100 SER cc_start: 0.8285 (t) cc_final: 0.7989 (p) REVERT: F 170 GLN cc_start: 0.8017 (mt0) cc_final: 0.7588 (tm-30) REVERT: F 405 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8343 (mmt180) REVERT: F 450 MET cc_start: 0.8970 (mmt) cc_final: 0.8239 (mmt) REVERT: G 39 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8391 (tm-30) REVERT: G 173 MET cc_start: 0.9026 (tpp) cc_final: 0.8782 (tpp) REVERT: G 316 TYR cc_start: 0.8698 (m-80) cc_final: 0.8288 (m-80) REVERT: G 380 ASP cc_start: 0.8345 (m-30) cc_final: 0.7915 (t0) REVERT: G 402 LEU cc_start: 0.8979 (mm) cc_final: 0.8755 (mt) REVERT: G 423 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8976 (mp) REVERT: G 510 TRP cc_start: 0.8340 (t-100) cc_final: 0.7987 (t-100) REVERT: G 513 MET cc_start: 0.8332 (tpp) cc_final: 0.8071 (tpt) REVERT: H 17 MET cc_start: 0.9137 (tmm) cc_final: 0.8800 (tmm) REVERT: H 92 PRO cc_start: 0.8133 (Cg_exo) cc_final: 0.7858 (Cg_endo) REVERT: H 183 MET cc_start: 0.8960 (mtt) cc_final: 0.8753 (mtp) REVERT: H 215 TYR cc_start: 0.8428 (m-80) cc_final: 0.8110 (m-80) REVERT: H 258 ASN cc_start: 0.7934 (m110) cc_final: 0.7378 (m-40) REVERT: H 261 MET cc_start: 0.8739 (mmm) cc_final: 0.8436 (mmt) REVERT: H 271 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8747 (mt) REVERT: H 277 TYR cc_start: 0.8592 (m-80) cc_final: 0.8325 (m-80) REVERT: H 300 LEU cc_start: 0.8948 (mt) cc_final: 0.8737 (mt) REVERT: I 41 LYS cc_start: 0.8706 (tppt) cc_final: 0.8458 (tppt) REVERT: I 49 ASP cc_start: 0.8336 (m-30) cc_final: 0.8025 (p0) REVERT: I 50 MET cc_start: 0.6059 (mmm) cc_final: 0.5638 (mmm) REVERT: I 89 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: I 94 SER cc_start: 0.9141 (p) cc_final: 0.8803 (p) REVERT: I 110 GLU cc_start: 0.8216 (tp30) cc_final: 0.7579 (tp30) REVERT: I 208 ASP cc_start: 0.8469 (t0) cc_final: 0.7974 (t70) REVERT: P 76 MET cc_start: 0.7660 (mtp) cc_final: 0.7090 (ptp) REVERT: P 113 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8150 (tmmt) REVERT: P 121 GLN cc_start: 0.8987 (mt0) cc_final: 0.8714 (mt0) REVERT: P 213 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7835 (t80) REVERT: P 220 TYR cc_start: 0.6815 (m-10) cc_final: 0.6468 (m-10) REVERT: P 254 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8152 (ttmt) REVERT: P 310 PHE cc_start: 0.5435 (OUTLIER) cc_final: 0.4460 (m-80) REVERT: P 311 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7028 (pm20) REVERT: P 340 VAL cc_start: 0.8029 (p) cc_final: 0.7778 (p) REVERT: Q 164 PHE cc_start: 0.8674 (m-10) cc_final: 0.8314 (m-10) REVERT: T 114 ASP cc_start: 0.8357 (m-30) cc_final: 0.7799 (t0) REVERT: T 117 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7971 (mp0) REVERT: T 139 MET cc_start: 0.5763 (mmm) cc_final: 0.5518 (tpp) REVERT: V 67 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8145 (ttmm) REVERT: V 81 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8687 (mp) REVERT: W 37 GLU cc_start: 0.9029 (tp30) cc_final: 0.8499 (tp30) REVERT: W 58 THR cc_start: 0.8597 (m) cc_final: 0.8389 (p) REVERT: Z 33 TYR cc_start: 0.7681 (m-80) cc_final: 0.7455 (m-10) REVERT: Z 50 MET cc_start: 0.8529 (tpp) cc_final: 0.8260 (tpp) REVERT: Z 94 GLU cc_start: 0.7915 (tt0) cc_final: 0.7587 (tt0) REVERT: Z 97 ILE cc_start: 0.7075 (mt) cc_final: 0.6851 (mt) REVERT: a 1 MET cc_start: 0.5499 (mmt) cc_final: 0.5007 (mtt) REVERT: b 10 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8023 (mttm) REVERT: b 32 MET cc_start: 0.8655 (mmt) cc_final: 0.8445 (mmt) REVERT: q 85 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: r 11 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6396 (tt) REVERT: r 101 MET cc_start: 0.8798 (ttp) cc_final: 0.8577 (ttt) outliers start: 125 outliers final: 93 residues processed: 803 average time/residue: 0.1974 time to fit residues: 258.5143 Evaluate side-chains 804 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 700 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 405 ARG Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 566 ILE 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 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 310 PHE Chi-restraints excluded: chain P residue 315 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 142 GLN Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 116 TRP Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 85 GLU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 387 optimal weight: 1.9990 chunk 255 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 313 optimal weight: 0.0770 chunk 307 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 365 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 361 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- 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 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN F 44 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 GLN S 73 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 HIS V 110 ASN Z 55 GLN ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN s 49 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.154526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.117967 restraints weight = 54531.068| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.54 r_work: 0.3463 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 34860 Z= 0.146 Angle : 0.845 75.265 47266 Z= 0.325 Chirality : 0.043 0.275 5152 Planarity : 0.005 0.132 5985 Dihedral : 8.657 132.394 4911 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 3.08 % Allowed : 20.88 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: 0.03 (0.13), residues: 4136 helix: 1.05 (0.12), residues: 1864 sheet: -0.84 (0.26), residues: 379 loop : -0.79 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 135 TYR 0.027 0.001 TYR X 91 PHE 0.028 0.001 PHE E 52 TRP 0.018 0.001 TRP A 106 HIS 0.007 0.001 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00343 (34820) covalent geometry : angle 0.65123 (47176) SS BOND : bond 0.00474 ( 3) SS BOND : angle 3.71546 ( 6) hydrogen bonds : bond 0.03934 ( 1432) hydrogen bonds : angle 4.83467 ( 4152) metal coordination : bond 0.01691 ( 37) metal coordination : angle 12.74932 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 713 time to evaluate : 1.279 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 2 ASN cc_start: 0.8260 (m-40) cc_final: 0.7908 (m-40) REVERT: A 49 LEU cc_start: 0.7143 (tt) cc_final: 0.6794 (tp) REVERT: B 147 LYS cc_start: 0.8739 (tptt) cc_final: 0.8248 (ttpt) REVERT: B 213 LYS cc_start: 0.9090 (tttt) cc_final: 0.8796 (ttpt) REVERT: B 223 ARG cc_start: 0.8086 (mtt-85) cc_final: 0.7757 (mpt-90) REVERT: C 171 ASP cc_start: 0.8424 (t0) cc_final: 0.8145 (t0) REVERT: E 52 PHE cc_start: 0.7108 (t80) cc_final: 0.6832 (t80) REVERT: E 91 TRP cc_start: 0.6619 (t-100) cc_final: 0.6290 (t-100) REVERT: E 150 THR cc_start: 0.7652 (m) cc_final: 0.7239 (p) REVERT: E 155 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8329 (mm) REVERT: F 80 MET cc_start: 0.8784 (mmp) cc_final: 0.8403 (mmm) REVERT: F 100 SER cc_start: 0.8276 (t) cc_final: 0.7977 (p) REVERT: F 170 GLN cc_start: 0.7981 (mt0) cc_final: 0.7579 (tm-30) REVERT: F 405 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8357 (mmt180) REVERT: F 450 MET cc_start: 0.8960 (mmt) cc_final: 0.8229 (mmt) REVERT: G 39 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8328 (tm-30) REVERT: G 173 MET cc_start: 0.9040 (tpp) cc_final: 0.8799 (tpp) REVERT: G 209 TYR cc_start: 0.8279 (t80) cc_final: 0.8058 (t80) REVERT: G 316 TYR cc_start: 0.8738 (m-80) cc_final: 0.8318 (m-80) REVERT: G 380 ASP cc_start: 0.8209 (m-30) cc_final: 0.7768 (t0) REVERT: G 423 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8988 (mp) REVERT: G 513 MET cc_start: 0.8381 (tpp) cc_final: 0.8146 (tpt) REVERT: G 538 ARG cc_start: 0.7405 (mtp85) cc_final: 0.7167 (mpt-90) REVERT: G 544 MET cc_start: 0.8162 (ttt) cc_final: 0.7867 (ttm) REVERT: H 17 MET cc_start: 0.9114 (tmm) cc_final: 0.8750 (tmm) REVERT: H 92 PRO cc_start: 0.8134 (Cg_exo) cc_final: 0.7852 (Cg_endo) REVERT: H 183 MET cc_start: 0.8933 (mtt) cc_final: 0.8730 (mtp) REVERT: H 215 TYR cc_start: 0.8391 (m-80) cc_final: 0.8081 (m-80) REVERT: H 258 ASN cc_start: 0.7986 (m110) cc_final: 0.7554 (m-40) REVERT: H 271 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8748 (mt) REVERT: H 277 TYR cc_start: 0.8555 (m-80) cc_final: 0.8302 (m-80) REVERT: I 41 LYS cc_start: 0.8698 (tppt) cc_final: 0.8445 (tppt) REVERT: I 49 ASP cc_start: 0.8335 (m-30) cc_final: 0.8051 (p0) REVERT: I 50 MET cc_start: 0.6123 (mmm) cc_final: 0.5744 (mmm) REVERT: I 89 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: I 94 SER cc_start: 0.9149 (p) cc_final: 0.8829 (p) REVERT: I 110 GLU cc_start: 0.8157 (tp30) cc_final: 0.7510 (tp30) REVERT: I 208 ASP cc_start: 0.8458 (t0) cc_final: 0.7997 (t70) REVERT: P 76 MET cc_start: 0.7557 (mtp) cc_final: 0.7164 (ptp) REVERT: P 113 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8125 (tmmt) REVERT: P 121 GLN cc_start: 0.8997 (mt0) cc_final: 0.8728 (mt0) REVERT: P 210 GLU cc_start: 0.7529 (pm20) cc_final: 0.7262 (pm20) REVERT: P 213 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7983 (t80) REVERT: P 220 TYR cc_start: 0.6833 (m-10) cc_final: 0.6489 (m-10) REVERT: P 254 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8171 (ttmt) REVERT: P 310 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.4445 (m-80) REVERT: P 311 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7030 (pm20) REVERT: Q 88 GLN cc_start: 0.7554 (tt0) cc_final: 0.7216 (tt0) REVERT: Q 164 PHE cc_start: 0.8689 (m-10) cc_final: 0.8320 (m-10) REVERT: S 71 PHE cc_start: 0.8471 (m-10) cc_final: 0.8249 (m-10) REVERT: S 73 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: T 114 ASP cc_start: 0.8312 (m-30) cc_final: 0.7624 (t0) REVERT: T 117 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7957 (mp0) REVERT: V 67 LYS cc_start: 0.8612 (mmtp) cc_final: 0.8137 (ttmm) REVERT: V 81 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8699 (mp) REVERT: V 94 MET cc_start: 0.8172 (mmm) cc_final: 0.7728 (mtp) REVERT: W 58 THR cc_start: 0.8603 (m) cc_final: 0.7453 (p) REVERT: Z 33 TYR cc_start: 0.7684 (m-80) cc_final: 0.7463 (m-10) REVERT: Z 50 MET cc_start: 0.8579 (tpp) cc_final: 0.8361 (tpp) REVERT: Z 94 GLU cc_start: 0.7879 (tt0) cc_final: 0.7656 (pt0) REVERT: Z 97 ILE cc_start: 0.7122 (mt) cc_final: 0.6838 (mt) REVERT: a 1 MET cc_start: 0.5657 (mmt) cc_final: 0.5191 (mtt) REVERT: b 10 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8214 (mttm) REVERT: q 85 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: r 9 GLN cc_start: 0.6983 (mt0) cc_final: 0.6712 (mp10) REVERT: r 101 MET cc_start: 0.8807 (ttp) cc_final: 0.8583 (ttt) outliers start: 112 outliers final: 91 residues processed: 780 average time/residue: 0.1988 time to fit residues: 251.7956 Evaluate side-chains 793 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 691 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 405 ARG Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 429 VAL Chi-restraints excluded: chain G residue 566 ILE 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 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 310 PHE Chi-restraints excluded: chain P residue 315 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 142 GLN Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 116 TRP Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 85 GLU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 321 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 285 optimal weight: 0.1980 chunk 281 optimal weight: 0.9980 chunk 402 optimal weight: 10.0000 chunk 389 optimal weight: 2.9990 chunk 394 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN F 44 ASN F 116 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN S 73 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 HIS V 110 ASN X 124 GLN ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN s 41 ASN s 49 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.153021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115938 restraints weight = 55063.803| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.47 r_work: 0.3345 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 34860 Z= 0.185 Angle : 0.872 75.048 47266 Z= 0.339 Chirality : 0.045 0.273 5152 Planarity : 0.005 0.132 5985 Dihedral : 8.680 132.651 4911 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 3.14 % Allowed : 21.10 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: 0.02 (0.13), residues: 4136 helix: 1.05 (0.12), residues: 1852 sheet: -0.92 (0.27), residues: 387 loop : -0.78 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 61 TYR 0.035 0.002 TYR H 142 PHE 0.029 0.002 PHE E 52 TRP 0.019 0.001 TRP A 106 HIS 0.007 0.001 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00443 (34820) covalent geometry : angle 0.67488 (47176) SS BOND : bond 0.01030 ( 3) SS BOND : angle 5.34657 ( 6) hydrogen bonds : bond 0.04120 ( 1432) hydrogen bonds : angle 4.89321 ( 4152) metal coordination : bond 0.02243 ( 37) metal coordination : angle 13.04679 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 712 time to evaluate : 1.287 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: A 2 ASN cc_start: 0.8212 (m-40) cc_final: 0.7883 (m-40) REVERT: A 49 LEU cc_start: 0.7123 (tt) cc_final: 0.6807 (tp) REVERT: B 147 LYS cc_start: 0.8595 (tptt) cc_final: 0.8126 (ttpt) REVERT: B 213 LYS cc_start: 0.8982 (tttt) cc_final: 0.8655 (ttpt) REVERT: B 223 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7706 (mpt-90) REVERT: C 171 ASP cc_start: 0.8397 (t0) cc_final: 0.8164 (t0) REVERT: D 437 LYS cc_start: 0.8230 (mttp) cc_final: 0.7959 (tmtt) REVERT: D 443 MET cc_start: 0.7834 (mmt) cc_final: 0.7467 (mtp) REVERT: E 61 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7414 (mtm-85) REVERT: E 150 THR cc_start: 0.7647 (m) cc_final: 0.7229 (p) REVERT: E 155 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8314 (mm) REVERT: F 80 MET cc_start: 0.8801 (mmp) cc_final: 0.8419 (mmm) REVERT: F 100 SER cc_start: 0.8291 (t) cc_final: 0.7971 (p) REVERT: F 374 TYR cc_start: 0.8709 (m-80) cc_final: 0.8312 (m-10) REVERT: F 403 ASP cc_start: 0.6636 (m-30) cc_final: 0.6264 (t0) REVERT: F 405 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8320 (mmt180) REVERT: F 450 MET cc_start: 0.8944 (mmt) cc_final: 0.8231 (mmt) REVERT: G 39 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8260 (tm-30) REVERT: G 97 MET cc_start: 0.7207 (pmm) cc_final: 0.6357 (pmm) REVERT: G 173 MET cc_start: 0.9034 (tpp) cc_final: 0.8768 (tpp) REVERT: G 209 TYR cc_start: 0.8202 (t80) cc_final: 0.7926 (t80) REVERT: G 333 PHE cc_start: 0.8043 (m-80) cc_final: 0.7020 (m-80) REVERT: G 380 ASP cc_start: 0.8289 (m-30) cc_final: 0.7787 (t0) REVERT: G 423 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9035 (mp) REVERT: G 513 MET cc_start: 0.8401 (tpp) cc_final: 0.8079 (tpt) REVERT: G 544 MET cc_start: 0.7988 (ttt) cc_final: 0.7688 (ttm) REVERT: H 17 MET cc_start: 0.9097 (tmm) cc_final: 0.8744 (tmm) REVERT: H 92 PRO cc_start: 0.8099 (Cg_exo) cc_final: 0.7823 (Cg_endo) REVERT: H 181 MET cc_start: 0.8248 (mtm) cc_final: 0.7954 (mtm) REVERT: H 183 MET cc_start: 0.8807 (mtt) cc_final: 0.8578 (mtp) REVERT: H 215 TYR cc_start: 0.8360 (m-80) cc_final: 0.8046 (m-80) REVERT: H 271 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8664 (mt) REVERT: H 277 TYR cc_start: 0.8463 (m-80) cc_final: 0.8151 (m-80) REVERT: I 41 LYS cc_start: 0.8612 (tppt) cc_final: 0.8356 (tppt) REVERT: I 49 ASP cc_start: 0.8246 (m-30) cc_final: 0.8046 (p0) REVERT: I 89 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: I 94 SER cc_start: 0.9070 (p) cc_final: 0.8753 (p) REVERT: I 208 ASP cc_start: 0.8534 (t0) cc_final: 0.8083 (t70) REVERT: P 76 MET cc_start: 0.7400 (mtp) cc_final: 0.7067 (ptp) REVERT: P 113 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8113 (tmmt) REVERT: P 121 GLN cc_start: 0.8998 (mt0) cc_final: 0.8709 (mt0) REVERT: P 210 GLU cc_start: 0.7701 (pm20) cc_final: 0.7428 (pm20) REVERT: P 220 TYR cc_start: 0.6916 (m-10) cc_final: 0.6560 (m-10) REVERT: P 254 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8126 (ttmt) REVERT: P 310 PHE cc_start: 0.5331 (OUTLIER) cc_final: 0.4403 (m-80) REVERT: P 311 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7037 (pm20) REVERT: Q 124 MET cc_start: 0.8360 (ttm) cc_final: 0.7737 (ttm) REVERT: Q 164 PHE cc_start: 0.8694 (m-10) cc_final: 0.8418 (m-10) REVERT: R 75 ARG cc_start: 0.7369 (mmp-170) cc_final: 0.6957 (tpm170) REVERT: S 64 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7169 (mtmt) REVERT: S 71 PHE cc_start: 0.8409 (m-10) cc_final: 0.8161 (m-10) REVERT: T 114 ASP cc_start: 0.8236 (m-30) cc_final: 0.7596 (t0) REVERT: T 117 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7916 (mp0) REVERT: T 120 MET cc_start: 0.7556 (mtm) cc_final: 0.7269 (mtp) REVERT: T 139 MET cc_start: 0.5978 (tpp) cc_final: 0.5567 (mmm) REVERT: V 67 LYS cc_start: 0.8578 (mmtp) cc_final: 0.8119 (ttmm) REVERT: V 81 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8627 (mp) REVERT: V 94 MET cc_start: 0.8109 (mmm) cc_final: 0.7631 (mtp) REVERT: W 43 TYR cc_start: 0.8653 (t80) cc_final: 0.8329 (t80) REVERT: W 58 THR cc_start: 0.8637 (m) cc_final: 0.8376 (p) REVERT: Z 33 TYR cc_start: 0.7658 (m-80) cc_final: 0.7457 (m-10) REVERT: Z 50 MET cc_start: 0.8467 (tpp) cc_final: 0.8253 (tpp) REVERT: Z 71 LEU cc_start: 0.8972 (mt) cc_final: 0.8742 (mt) REVERT: Z 97 ILE cc_start: 0.7198 (mt) cc_final: 0.6866 (mt) REVERT: a 1 MET cc_start: 0.5671 (mmt) cc_final: 0.5327 (mtt) REVERT: b 10 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8073 (mttm) REVERT: b 40 LYS cc_start: 0.8711 (pttt) cc_final: 0.8285 (ptpt) REVERT: q 85 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: r 9 GLN cc_start: 0.7122 (mt0) cc_final: 0.6808 (mp10) REVERT: r 101 MET cc_start: 0.8756 (ttp) cc_final: 0.8538 (ttt) outliers start: 114 outliers final: 93 residues processed: 779 average time/residue: 0.2072 time to fit residues: 262.1158 Evaluate side-chains 781 residues out of total 3635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 679 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 405 ARG Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 429 VAL Chi-restraints excluded: chain G residue 566 ILE 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 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 310 PHE Chi-restraints excluded: chain P residue 315 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 36 PHE Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 142 GLN Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 116 TRP Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 85 GLU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 16 SER Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 382 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 396 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 149 optimal weight: 0.0570 chunk 147 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 HIS V 110 ASN W 61 GLN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** b 69 HIS ** 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 = 0.4062 r_free = 0.4062 target = 0.153925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117119 restraints weight = 54443.155| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.53 r_work: 0.3450 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 34860 Z= 0.146 Angle : 0.868 74.958 47266 Z= 0.338 Chirality : 0.044 0.270 5152 Planarity : 0.005 0.131 5985 Dihedral : 8.671 132.804 4911 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 3.11 % Allowed : 21.35 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: 0.03 (0.13), residues: 4136 helix: 1.01 (0.12), residues: 1858 sheet: -0.83 (0.27), residues: 377 loop : -0.75 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 61 TYR 0.044 0.002 TYR H 142 PHE 0.031 0.002 PHE P 213 TRP 0.019 0.001 TRP A 106 HIS 0.012 0.001 HIS b 69 Details of bonding type rmsd covalent geometry : bond 0.00346 (34820) covalent geometry : angle 0.67402 (47176) SS BOND : bond 0.00349 ( 3) SS BOND : angle 5.32481 ( 6) hydrogen bonds : bond 0.04008 ( 1432) hydrogen bonds : angle 4.87788 ( 4152) metal coordination : bond 0.01705 ( 37) metal coordination : angle 12.91738 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11040.68 seconds wall clock time: 189 minutes 3.15 seconds (11343.15 seconds total)