Starting phenix.real_space_refine on Mon Jul 6 06:29:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnr_38512/07_2026/8xnr_38512_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnr_38512/07_2026/8xnr_38512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnr_38512/07_2026/8xnr_38512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnr_38512/07_2026/8xnr_38512.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnr_38512/07_2026/8xnr_38512_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnr_38512/07_2026/8xnr_38512_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.087 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 10 5.49 5 S 244 5.16 5 C 21714 2.51 5 N 5772 2.21 5 O 6142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33911 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: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2495 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 22, 'TRANS': 289} 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: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UQ1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'3PE': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1014 SG CYS B 99 80.933 59.527 105.344 1.00 29.52 S ATOM 1517 SG CYS B 164 78.169 56.220 110.458 1.00 28.96 S ATOM 1747 SG CYS B 194 83.316 56.018 109.675 1.00 29.28 S ATOM 1020 SG CYS B 100 79.595 55.548 104.660 1.00 30.11 S ATOM 7534 SG CYS E 134 140.904 51.908 151.730 1.00 56.01 S ATOM 7568 SG CYS E 139 143.395 53.492 150.935 1.00 56.50 S ATOM 7852 SG CYS E 175 138.563 55.477 154.271 1.00 54.42 S ATOM 7875 SG CYS E 179 141.876 57.129 154.316 1.00 57.95 S ATOM 11405 SG CYS F 425 122.287 61.361 154.408 1.00 45.60 S ATOM 11083 SG CYS F 385 122.270 58.693 148.700 1.00 39.95 S ATOM 11063 SG CYS F 382 118.027 59.964 150.954 1.00 40.29 S ATOM 11044 SG CYS F 379 119.975 55.980 153.939 1.00 43.09 S ATOM 12453 SG CYS G 131 101.662 48.505 137.889 1.00 31.31 S ATOM 12432 SG CYS G 128 103.677 52.181 133.163 1.00 30.26 S ATOM 12493 SG CYS G 137 101.385 54.453 139.127 1.00 33.13 S ATOM 13178 SG CYS G 226 103.245 48.768 146.464 1.00 34.31 S ATOM 12849 SG CYS G 182 106.408 47.248 152.251 1.00 36.31 S ATOM 12825 SG CYS G 179 105.819 52.750 149.538 1.00 35.62 S ATOM 12802 SG CYS G 176 109.213 48.378 147.184 1.00 34.05 S ATOM 11939 SG CYS G 64 107.290 58.838 151.354 1.00 35.53 S ATOM 12025 SG CYS G 75 108.023 60.822 149.622 1.00 36.47 S ATOM 12050 SG CYS G 78 106.964 65.344 151.600 1.00 36.76 S ATOM 12151 SG CYS G 92 106.745 63.541 154.839 1.00 39.04 S ATOM 20136 SG CYS I 123 87.249 51.134 118.905 1.00 27.30 S ATOM 20362 SG CYS I 152 86.989 49.812 113.831 1.00 27.39 S ATOM 20409 SG CYS I 158 92.653 49.998 115.925 1.00 26.60 S ATOM 20388 SG CYS I 155 89.577 54.428 115.473 1.00 27.04 S ATOM 20085 SG CYS I 116 97.076 47.247 126.400 1.00 29.24 S ATOM 20108 SG CYS I 119 92.703 46.849 123.060 1.00 28.85 S ATOM 20066 SG CYS I 113 95.890 42.021 123.293 1.00 28.61 S ATOM 20438 SG CYS I 162 98.811 46.538 121.048 1.00 28.07 S ATOM 24947 SG CYS R 79 112.277 39.876 125.863 1.00 32.60 S ATOM 25123 SG CYS R 104 109.814 38.510 127.356 1.00 32.49 S ATOM 25145 SG CYS R 107 109.142 39.058 123.914 1.00 30.78 S Time building chain proxies: 6.84, per 1000 atoms: 0.20 Number of scatterers: 33911 At special positions: 0 Unit cell: (168.3, 128.7, 202.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 244 16.00 P 10 15.00 O 6142 8.00 N 5772 7.00 C 21714 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: 3.18 Conformation dependent library (CDL) restraints added in 1.5 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 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 116 " pdb="FE2 SF4 I 303 " - 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 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7830 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 31 sheets defined 49.9% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 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: 3.587A 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: 4.117A 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: 3.854A 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 138 removed outlier: 3.770A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 138' Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.753A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.008A 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: 3.660A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 3.690A 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: 3.745A 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: 3.669A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.531A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.470A 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: 3.553A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.086A 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: 3.515A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.610A 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: 3.565A 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: 3.873A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 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 333 removed outlier: 4.156A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 removed outlier: 3.507A pdb=" N VAL F 343 " --> pdb=" O PHE F 339 " (cutoff:3.500A) 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: 3.663A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.914A 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: 4.348A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.519A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.598A 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: 3.680A 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: 4.025A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.007A 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: 3.641A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.300A 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: 3.682A 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: 3.573A 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: 3.569A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.999A 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: 3.897A 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: 3.539A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.529A 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: 4.026A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.277A 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: 3.624A 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: 3.611A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 219 removed outlier: 4.081A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 222 No H-bonds generated for 'chain 'P' and resid 220 through 222' Processing helix chain 'P' and resid 229 through 232 Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 272 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.621A 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: 4.413A 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: 4.199A 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: 3.624A 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: 3.615A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 97 Processing helix chain 'W' and resid 98 through 100 No H-bonds generated for 'chain 'W' and resid 98 through 100' Processing helix chain 'W' and resid 102 through 108 removed outlier: 3.642A pdb=" N ARG W 108 " --> pdb=" O THR W 104 " (cutoff:3.500A) 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: 3.528A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.624A 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: 4.463A 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: 3.906A 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: 4.500A 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: 4.289A 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: 3.664A 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: 6.371A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.920A 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: 6.933A 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: 6.795A 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 78 removed outlier: 3.523A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 83 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LYS C 143 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.570A 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: 6.708A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.002A 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: 4.254A 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: 3.727A 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: 5.542A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.374A 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 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: 6.231A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.753A 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: 6.152A 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: 6.956A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 32 through 34 Processing sheet with id=AB4, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.868A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.313A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AB8, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.454A 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=AB9, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.202A 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=AC1, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC3, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.408A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.361A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC6, 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=AC6 Processing sheet with id=AC7, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AC8, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AC9, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD1, 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=AD2, 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=AD3, first strand: chain 'X' and resid 129 through 130 Processing sheet with id=AD4, 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: 3.645A 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) 1428 hydrogen bonds defined for protein. 4137 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: 7.18 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 11469 1.37 - 1.59: 22786 1.59 - 1.80: 261 1.80 - 2.02: 130 2.02 - 2.23: 80 Bond restraints: 34726 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 1.33e+03 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.398 -0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C15 EHZ W 201 " pdb=" O4 EHZ W 201 " ideal model delta sigma weight residual 1.356 1.180 0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" C VAL W 106 " pdb=" N MET W 107 " ideal model delta sigma weight residual 1.335 1.218 0.117 1.34e-02 5.57e+03 7.68e+01 bond pdb=" CA ASP R 39 " pdb=" C ASP R 39 " ideal model delta sigma weight residual 1.527 1.639 -0.112 1.41e-02 5.03e+03 6.28e+01 ... (remaining 34721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.67: 46319 6.67 - 13.34: 577 13.34 - 20.01: 156 20.01 - 26.68: 3 26.68 - 33.35: 2 Bond angle restraints: 47057 Sorted by residual: angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.01 25.63 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 93.50 19.67 1.26e+00 6.30e-01 2.44e+02 angle pdb=" N ILE G 251 " pdb=" CA ILE G 251 " pdb=" C ILE G 251 " ideal model delta sigma weight residual 108.17 126.85 -18.68 1.40e+00 5.10e-01 1.78e+02 angle pdb=" N MET G 77 " pdb=" CA MET G 77 " pdb=" C MET G 77 " ideal model delta sigma weight residual 113.38 97.32 16.06 1.23e+00 6.61e-01 1.70e+02 angle pdb=" S1 FES G 803 " pdb="FE2 FES G 803 " pdb=" S2 FES G 803 " ideal model delta sigma weight residual 104.33 89.74 14.59 1.14e+00 7.69e-01 1.64e+02 ... (remaining 47052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.82: 20186 26.82 - 53.63: 659 53.63 - 80.45: 86 80.45 - 107.26: 9 107.26 - 134.08: 4 Dihedral angle restraints: 20944 sinusoidal: 8799 harmonic: 12145 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.49 -68.49 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" C LEU G 387 " pdb=" N LEU G 387 " pdb=" CA LEU G 387 " pdb=" CB LEU G 387 " ideal model delta harmonic sigma weight residual -122.60 -105.68 -16.92 0 2.50e+00 1.60e-01 4.58e+01 dihedral pdb=" CB CYS S 24 " pdb=" SG CYS S 24 " pdb=" SG CYS S 58 " pdb=" CB CYS S 58 " ideal model delta sinusoidal sigma weight residual -86.00 -139.95 53.95 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 20941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4555 0.183 - 0.367: 516 0.367 - 0.550: 45 0.550 - 0.734: 3 0.734 - 0.917: 24 Chirality restraints: 5143 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 2.10e+01 chirality pdb="FE3 SF4 I 303 " pdb=" S1 SF4 I 303 " pdb=" S2 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.91 2.00e-01 2.50e+01 2.09e+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 2.05e+01 ... (remaining 5140 not shown) Planarity restraints: 5975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ9 H 401 " -0.343 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C18 UQ9 H 401 " 0.509 2.00e-02 2.50e+03 pdb=" C19 UQ9 H 401 " 0.110 2.00e-02 2.50e+03 pdb=" C20 UQ9 H 401 " -0.135 2.00e-02 2.50e+03 pdb=" C21 UQ9 H 401 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 UQ9 H 401 " -0.304 2.00e-02 2.50e+03 2.58e-01 8.30e+02 pdb=" C23 UQ9 H 401 " 0.438 2.00e-02 2.50e+03 pdb=" C24 UQ9 H 401 " 0.099 2.00e-02 2.50e+03 pdb=" C25 UQ9 H 401 " -0.045 2.00e-02 2.50e+03 pdb=" C26 UQ9 H 401 " -0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 401 " 0.022 2.00e-02 2.50e+03 1.60e-01 7.69e+02 pdb=" C1M UQ9 H 401 " 0.110 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 401 " -0.020 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 401 " -0.044 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 401 " 0.080 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 401 " -0.095 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 401 " -0.004 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " 0.081 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 401 " -0.030 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 401 " -0.173 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 401 " 0.380 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 401 " -0.309 2.00e-02 2.50e+03 ... (remaining 5972 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 74 2.38 - 3.01: 22919 3.01 - 3.64: 53065 3.64 - 4.27: 83791 4.27 - 4.90: 135149 Nonbonded interactions: 294998 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 294993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 39.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.141 34766 Z= 1.039 Angle : 2.248 52.604 47147 Z= 1.492 Chirality : 0.130 0.917 5143 Planarity : 0.010 0.292 5975 Dihedral : 13.142 134.079 13105 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 43.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 0.28 % Allowed : 7.77 % Favored : 91.96 % Cbeta Deviations : 1.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.12), residues: 4131 helix: -0.83 (0.11), residues: 1797 sheet: -1.12 (0.29), residues: 337 loop : -2.04 (0.12), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 333 TYR 0.046 0.002 TYR B 112 PHE 0.032 0.002 PHE G 462 TRP 0.034 0.002 TRP G 285 HIS 0.017 0.002 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.01454 / 0.93 (34726) covalent geometry : angle 2.11763 / 1.49 (47057) SS BOND : bond 0.00744 / 0.38 ( 3) SS BOND : angle 2.19403 / 1.09 ( 6) hydrogen bonds : bond 0.24737 / 16.22 ( 1428) hydrogen bonds : angle 8.96257 / 6.33 ( 4137) metal coordination : bond 0.52294 / 33.81 ( 37) metal coordination : angle 17.98818 / 13.53 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1559 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1549 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.8250 (m-80) cc_final: 0.7895 (m-80) REVERT: C 137 ASN cc_start: 0.8639 (t0) cc_final: 0.8322 (t0) REVERT: C 168 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6694 (tm-30) REVERT: D 145 MET cc_start: 0.7789 (mtt) cc_final: 0.7378 (mtt) REVERT: F 163 TYR cc_start: 0.6240 (t80) cc_final: 0.5947 (t80) REVERT: F 204 TYR cc_start: 0.7738 (t80) cc_final: 0.7280 (t80) REVERT: G 213 MET cc_start: 0.7731 (ptm) cc_final: 0.7531 (ptm) REVERT: G 295 ASP cc_start: 0.7919 (m-30) cc_final: 0.7668 (m-30) REVERT: G 528 LEU cc_start: 0.9134 (mt) cc_final: 0.8870 (mp) REVERT: G 654 VAL cc_start: 0.8185 (p) cc_final: 0.7923 (p) REVERT: H 181 MET cc_start: 0.7629 (mtt) cc_final: 0.7271 (mtt) REVERT: H 282 TYR cc_start: 0.7436 (t80) cc_final: 0.7120 (t80) REVERT: H 285 LEU cc_start: 0.8528 (tt) cc_final: 0.7617 (tt) REVERT: I 64 THR cc_start: 0.8160 (p) cc_final: 0.7938 (t) REVERT: I 145 TYR cc_start: 0.8485 (t80) cc_final: 0.7945 (t80) REVERT: Q 87 MET cc_start: 0.7778 (mmt) cc_final: 0.7514 (mmt) REVERT: Q 96 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8271 (mmtt) REVERT: T 84 LEU cc_start: 0.8169 (mt) cc_final: 0.7428 (mp) REVERT: T 86 VAL cc_start: 0.8181 (t) cc_final: 0.7935 (t) REVERT: T 138 LEU cc_start: 0.8275 (pp) cc_final: 0.7986 (pp) REVERT: V 100 TRP cc_start: 0.7290 (p90) cc_final: 0.7054 (p90) REVERT: W 27 ASP cc_start: 0.6862 (p0) cc_final: 0.6119 (p0) REVERT: W 39 TYR cc_start: 0.8686 (t80) cc_final: 0.8482 (t80) REVERT: Z 116 TRP cc_start: 0.6817 (t-100) cc_final: 0.6319 (t-100) REVERT: a 59 ARG cc_start: 0.6819 (ppt170) cc_final: 0.6555 (ppt170) REVERT: b 32 MET cc_start: 0.7644 (mmm) cc_final: 0.7402 (mmm) REVERT: q 144 TYR cc_start: 0.3433 (m-80) cc_final: 0.3228 (m-80) outliers start: 10 outliers final: 2 residues processed: 1553 average time/residue: 0.2395 time to fit residues: 585.7499 Evaluate side-chains 910 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 907 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain Q residue 96 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.0670 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN B 166 ASN B 209 GLN C 54 HIS C 56 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 179 ASN C 195 HIS D 79 ASN D 117 HIS D 131 GLN D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN D 346 GLN D 381 HIS D 454 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS E 152 GLN E 190 ASN E 245 GLN F 44 ASN F 277 ASN F 376 HIS ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 GLN G 260 ASN G 331 GLN ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 HIS G 460 HIS G 495 ASN G 569 GLN G 571 HIS G 604 GLN G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 97 ASN H 163 GLN H 169 GLN H 171 HIS H 235 ASN H 292 ASN I 126 GLN I 159 GLN P 238 GLN P 251 ASN P 323 HIS P 341 GLN Q 71 HIS R 33 HIS ** S 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 HIS W 111 HIS X 73 GLN X 99 HIS Z 85 GLN Z 90 ASN ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN 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 s 41 ASN s 59 GLN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.126156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096956 restraints weight = 69039.526| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.09 r_work: 0.3246 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 34766 Z= 0.225 Angle : 0.990 65.469 47147 Z= 0.425 Chirality : 0.050 0.284 5143 Planarity : 0.006 0.119 5975 Dihedral : 9.509 143.212 4863 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.74 % Favored : 97.24 % Rotamer: Outliers : 4.13 % Allowed : 16.28 % Favored : 79.59 % 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: -0.93 (0.13), residues: 4131 helix: 0.24 (0.12), residues: 1863 sheet: -1.07 (0.26), residues: 363 loop : -1.35 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 68 TYR 0.025 0.002 TYR T 90 PHE 0.038 0.003 PHE H 223 TRP 0.024 0.002 TRP A 113 HIS 0.013 0.002 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (34726) covalent geometry : angle 0.81916 / 0.42 (47057) SS BOND : bond 0.02090 / 1.00 ( 3) SS BOND : angle 3.00103 / 1.48 ( 6) hydrogen bonds : bond 0.05811 / 3.84 ( 1428) hydrogen bonds : angle 5.77958 / 4.08 ( 4137) metal coordination : bond 0.03107 / 1.91 ( 37) metal coordination : angle 13.17632 / 9.56 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1012 time to evaluate : 1.249 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: A 2 ASN cc_start: 0.8358 (m-40) cc_final: 0.8085 (m-40) REVERT: A 92 PHE cc_start: 0.9005 (m-10) cc_final: 0.8775 (m-10) REVERT: B 219 LYS cc_start: 0.8450 (tttm) cc_final: 0.8213 (tptp) REVERT: C 70 LYS cc_start: 0.9060 (tttt) cc_final: 0.8843 (tttp) REVERT: C 168 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7802 (tm-30) REVERT: C 184 ARG cc_start: 0.8740 (ptp90) cc_final: 0.8460 (ptt90) REVERT: D 120 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8819 (m) REVERT: D 145 MET cc_start: 0.8431 (mtt) cc_final: 0.8086 (mtt) REVERT: D 185 MET cc_start: 0.8810 (tpt) cc_final: 0.8262 (tpp) REVERT: E 59 TYR cc_start: 0.7637 (m-80) cc_final: 0.7308 (m-80) REVERT: E 61 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7349 (ttm110) REVERT: E 105 GLN cc_start: 0.8340 (mp10) cc_final: 0.8068 (mp10) REVERT: E 129 TYR cc_start: 0.7726 (m-80) cc_final: 0.7252 (m-10) REVERT: E 132 GLN cc_start: 0.8108 (mt0) cc_final: 0.7006 (mt0) REVERT: E 143 ASP cc_start: 0.8330 (m-30) cc_final: 0.8121 (t0) REVERT: E 168 PHE cc_start: 0.8753 (m-80) cc_final: 0.8432 (m-10) REVERT: E 192 TYR cc_start: 0.8280 (m-80) cc_final: 0.7843 (m-80) REVERT: E 242 PHE cc_start: 0.8105 (t80) cc_final: 0.7823 (t80) REVERT: F 75 TRP cc_start: 0.7503 (t60) cc_final: 0.7129 (t60) REVERT: F 102 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7273 (ttp) REVERT: F 115 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8555 (m) REVERT: F 177 TYR cc_start: 0.7520 (m-80) cc_final: 0.7061 (m-10) REVERT: F 219 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8245 (mtmm) REVERT: F 338 ASP cc_start: 0.7944 (m-30) cc_final: 0.7596 (m-30) REVERT: F 383 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9037 (p) REVERT: F 390 ASP cc_start: 0.8455 (t0) cc_final: 0.8244 (t70) REVERT: F 418 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: F 433 TRP cc_start: 0.8763 (m-10) cc_final: 0.8297 (m-90) REVERT: G 97 MET cc_start: 0.8122 (mtp) cc_final: 0.7836 (mtm) REVERT: G 138 ASP cc_start: 0.8544 (m-30) cc_final: 0.7940 (t0) REVERT: G 224 ASP cc_start: 0.8271 (m-30) cc_final: 0.7667 (m-30) REVERT: G 265 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8796 (t) REVERT: G 284 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: G 476 LEU cc_start: 0.9321 (tp) cc_final: 0.9110 (tp) REVERT: G 496 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8282 (tmm) REVERT: G 636 TYR cc_start: 0.8248 (p90) cc_final: 0.8035 (p90) REVERT: H 282 TYR cc_start: 0.8052 (t80) cc_final: 0.7837 (t80) REVERT: I 51 LYS cc_start: 0.8177 (tppt) cc_final: 0.7867 (mmpt) REVERT: I 70 LEU cc_start: 0.9163 (mp) cc_final: 0.8897 (mp) REVERT: I 145 TYR cc_start: 0.8971 (t80) cc_final: 0.8686 (t80) REVERT: I 208 ASP cc_start: 0.8298 (t0) cc_final: 0.7768 (t0) REVERT: P 76 MET cc_start: 0.8725 (mtp) cc_final: 0.8461 (mtt) REVERT: P 91 ILE cc_start: 0.8915 (tp) cc_final: 0.8651 (tp) REVERT: P 118 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8402 (tttp) REVERT: P 205 ASP cc_start: 0.8354 (p0) cc_final: 0.7970 (p0) REVERT: P 211 ASP cc_start: 0.7813 (p0) cc_final: 0.7379 (p0) REVERT: P 215 ASN cc_start: 0.8480 (m-40) cc_final: 0.7982 (m110) REVERT: P 283 MET cc_start: 0.6948 (mmm) cc_final: 0.6160 (mmm) REVERT: P 376 ASN cc_start: 0.5705 (t0) cc_final: 0.5024 (m-40) REVERT: P 377 TYR cc_start: 0.6115 (t80) cc_final: 0.5234 (t80) REVERT: Q 69 GLU cc_start: 0.8269 (tp30) cc_final: 0.6948 (tp30) REVERT: Q 107 TRP cc_start: 0.9141 (p90) cc_final: 0.8892 (p90) REVERT: T 84 LEU cc_start: 0.8928 (mt) cc_final: 0.8593 (mp) REVERT: T 111 ASP cc_start: 0.7167 (t0) cc_final: 0.6858 (t0) REVERT: T 114 ASP cc_start: 0.8476 (m-30) cc_final: 0.8234 (m-30) REVERT: T 130 ILE cc_start: 0.8652 (mp) cc_final: 0.8050 (mp) REVERT: V 69 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8335 (mt-10) REVERT: V 76 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8446 (mm-30) REVERT: V 94 MET cc_start: 0.8606 (mmm) cc_final: 0.8271 (mmm) REVERT: V 100 TRP cc_start: 0.7944 (p90) cc_final: 0.7656 (p90) REVERT: V 110 ASN cc_start: 0.8199 (m-40) cc_final: 0.7977 (m-40) REVERT: W 27 ASP cc_start: 0.7115 (p0) cc_final: 0.6345 (p0) REVERT: W 119 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8323 (mmtm) REVERT: X 42 GLU cc_start: 0.8797 (tt0) cc_final: 0.8473 (tt0) REVERT: X 59 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: X 73 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: X 85 TYR cc_start: 0.7336 (t80) cc_final: 0.6724 (t80) REVERT: X 121 ASP cc_start: 0.8100 (m-30) cc_final: 0.7892 (m-30) REVERT: Z 24 ASN cc_start: 0.8579 (t0) cc_final: 0.8375 (t0) REVERT: Z 36 PHE cc_start: 0.8944 (m-80) cc_final: 0.8742 (m-80) REVERT: Z 50 MET cc_start: 0.8371 (tpp) cc_final: 0.8063 (mmm) REVERT: Z 90 ASN cc_start: 0.8746 (m-40) cc_final: 0.8536 (m110) REVERT: Z 91 LEU cc_start: 0.9007 (tm) cc_final: 0.8778 (tp) REVERT: Z 116 TRP cc_start: 0.8187 (t-100) cc_final: 0.7889 (t-100) REVERT: Z 133 MET cc_start: 0.8151 (ttp) cc_final: 0.7694 (tpt) REVERT: a 35 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8179 (mt-10) REVERT: a 43 TYR cc_start: 0.8759 (t80) cc_final: 0.6261 (m-80) REVERT: a 59 ARG cc_start: 0.7323 (ppt170) cc_final: 0.6712 (ppt170) REVERT: a 60 TYR cc_start: 0.8246 (p90) cc_final: 0.8022 (p90) REVERT: b 10 LYS cc_start: 0.7279 (ttmt) cc_final: 0.6906 (ptmm) REVERT: b 34 MET cc_start: 0.7736 (mtt) cc_final: 0.7522 (mtt) REVERT: b 49 THR cc_start: 0.9240 (p) cc_final: 0.9036 (p) REVERT: q 132 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7534 (ttpt) outliers start: 150 outliers final: 61 residues processed: 1099 average time/residue: 0.2175 time to fit residues: 392.3938 Evaluate side-chains 869 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 796 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 206 CYS Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 669 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 118 LYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 157 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 144 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 132 LYS Chi-restraints excluded: chain r residue 101 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 185 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 297 optimal weight: 0.4980 chunk 367 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 307 optimal weight: 20.0000 chunk 336 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN B 166 ASN C 88 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 136 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN G 140 GLN G 388 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN I 193 ASN P 147 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN b 11 ASN q 12 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.120824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091572 restraints weight = 68496.074| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.86 r_work: 0.3148 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 34766 Z= 0.229 Angle : 0.933 70.233 47147 Z= 0.383 Chirality : 0.047 0.215 5143 Planarity : 0.006 0.124 5975 Dihedral : 9.161 136.420 4858 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 4.46 % Allowed : 18.24 % Favored : 77.30 % 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: -0.52 (0.13), residues: 4131 helix: 0.51 (0.12), residues: 1868 sheet: -0.97 (0.27), residues: 363 loop : -1.03 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 80 TYR 0.026 0.002 TYR Q 160 PHE 0.032 0.002 PHE B 95 TRP 0.019 0.002 TRP Q 166 HIS 0.007 0.001 HIS S 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (34726) covalent geometry : angle 0.73709 / 0.38 (47057) SS BOND : bond 0.01251 / 0.60 ( 3) SS BOND : angle 4.47029 / 2.09 ( 6) hydrogen bonds : bond 0.05033 / 3.31 ( 1428) hydrogen bonds : angle 5.35163 / 3.79 ( 4137) metal coordination : bond 0.03083 / 2.01 ( 37) metal coordination : angle 13.50204 / 9.76 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 862 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8736 (mm) cc_final: 0.8459 (mm) REVERT: B 181 CYS cc_start: 0.8554 (p) cc_final: 0.8185 (p) REVERT: C 70 LYS cc_start: 0.9104 (tttt) cc_final: 0.8846 (tttp) REVERT: C 168 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7951 (tm-30) REVERT: D 105 MET cc_start: 0.7710 (tpp) cc_final: 0.7306 (tpp) REVERT: D 145 MET cc_start: 0.8623 (mtt) cc_final: 0.8260 (mtt) REVERT: D 263 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9035 (m) REVERT: D 264 ASN cc_start: 0.8225 (m-40) cc_final: 0.7959 (p0) REVERT: E 59 TYR cc_start: 0.7853 (m-80) cc_final: 0.7480 (m-80) REVERT: E 69 TYR cc_start: 0.7842 (m-80) cc_final: 0.7217 (m-80) REVERT: E 88 GLN cc_start: 0.8043 (tt0) cc_final: 0.7839 (tt0) REVERT: E 105 GLN cc_start: 0.8314 (mp10) cc_final: 0.8025 (mp10) REVERT: E 159 VAL cc_start: 0.7304 (OUTLIER) cc_final: 0.6932 (p) REVERT: E 186 GLN cc_start: 0.7423 (pt0) cc_final: 0.7018 (pt0) REVERT: E 192 TYR cc_start: 0.8331 (m-80) cc_final: 0.7897 (m-80) REVERT: E 205 ASP cc_start: 0.8533 (m-30) cc_final: 0.7952 (p0) REVERT: E 242 PHE cc_start: 0.8027 (t80) cc_final: 0.7789 (t80) REVERT: F 102 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7228 (ttp) REVERT: F 157 TYR cc_start: 0.7696 (t80) cc_final: 0.7411 (t80) REVERT: F 204 TYR cc_start: 0.9030 (t80) cc_final: 0.8476 (t80) REVERT: F 248 VAL cc_start: 0.8900 (t) cc_final: 0.8660 (p) REVERT: F 383 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9032 (p) REVERT: F 414 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7384 (tm-30) REVERT: F 433 TRP cc_start: 0.8794 (m-10) cc_final: 0.8470 (m-10) REVERT: G 97 MET cc_start: 0.8429 (mtp) cc_final: 0.8229 (ttt) REVERT: G 123 ASN cc_start: 0.9575 (OUTLIER) cc_final: 0.9357 (m-40) REVERT: G 138 ASP cc_start: 0.8717 (m-30) cc_final: 0.8376 (t0) REVERT: G 254 MET cc_start: 0.8900 (mmm) cc_final: 0.8681 (mmm) REVERT: G 265 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8796 (t) REVERT: G 364 ASP cc_start: 0.7743 (m-30) cc_final: 0.7249 (t70) REVERT: G 367 CYS cc_start: 0.8320 (m) cc_final: 0.8049 (m) REVERT: G 476 LEU cc_start: 0.9388 (tp) cc_final: 0.9146 (tp) REVERT: G 489 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8535 (mp) REVERT: G 579 MET cc_start: 0.8623 (ptp) cc_final: 0.8123 (ppp) REVERT: G 618 GLU cc_start: 0.7566 (mp0) cc_final: 0.7214 (mp0) REVERT: H 54 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8696 (tttm) REVERT: H 246 LEU cc_start: 0.8445 (tp) cc_final: 0.8187 (mt) REVERT: H 279 ARG cc_start: 0.8888 (mtm110) cc_final: 0.8688 (mtm-85) REVERT: H 282 TYR cc_start: 0.8320 (t80) cc_final: 0.7895 (t80) REVERT: I 51 LYS cc_start: 0.8341 (tppt) cc_final: 0.8033 (mmpt) REVERT: I 70 LEU cc_start: 0.9119 (mp) cc_final: 0.8857 (mp) REVERT: I 208 ASP cc_start: 0.8542 (t0) cc_final: 0.7953 (t70) REVERT: P 76 MET cc_start: 0.8840 (mtp) cc_final: 0.8614 (mtt) REVERT: P 91 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8709 (tp) REVERT: P 118 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8336 (tttp) REVERT: P 205 ASP cc_start: 0.8416 (p0) cc_final: 0.7909 (p0) REVERT: P 211 ASP cc_start: 0.7932 (p0) cc_final: 0.7519 (p0) REVERT: P 215 ASN cc_start: 0.8370 (m-40) cc_final: 0.7922 (m110) REVERT: P 338 LEU cc_start: 0.7995 (mt) cc_final: 0.7657 (mp) REVERT: P 376 ASN cc_start: 0.5902 (t0) cc_final: 0.5172 (m-40) REVERT: P 377 TYR cc_start: 0.6042 (t80) cc_final: 0.5191 (t80) REVERT: Q 69 GLU cc_start: 0.8631 (tp30) cc_final: 0.7845 (tp30) REVERT: Q 73 LYS cc_start: 0.9073 (ptpt) cc_final: 0.8634 (ptpt) REVERT: T 84 LEU cc_start: 0.8909 (mt) cc_final: 0.8661 (mp) REVERT: T 111 ASP cc_start: 0.7535 (t0) cc_final: 0.7276 (t0) REVERT: T 114 ASP cc_start: 0.8696 (m-30) cc_final: 0.8404 (m-30) REVERT: T 147 TYR cc_start: 0.7794 (t80) cc_final: 0.7429 (t80) REVERT: V 44 TYR cc_start: 0.9005 (t80) cc_final: 0.8694 (t80) REVERT: V 76 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8429 (mm-30) REVERT: V 81 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8885 (mp) REVERT: V 94 MET cc_start: 0.8670 (mmm) cc_final: 0.8252 (mmm) REVERT: V 100 TRP cc_start: 0.8268 (p90) cc_final: 0.7803 (p90) REVERT: V 110 ASN cc_start: 0.8290 (m-40) cc_final: 0.8054 (m-40) REVERT: W 37 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7635 (mt-10) REVERT: W 45 GLU cc_start: 0.8478 (tp30) cc_final: 0.8034 (tp30) REVERT: W 48 ASN cc_start: 0.8624 (t0) cc_final: 0.8183 (t0) REVERT: W 60 LYS cc_start: 0.9026 (tptm) cc_final: 0.8650 (pttp) REVERT: W 72 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8631 (ttpp) REVERT: W 94 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8664 (tp40) REVERT: X 16 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7907 (tm-30) REVERT: X 44 MET cc_start: 0.8657 (mmt) cc_final: 0.8313 (tpp) REVERT: X 56 CYS cc_start: 0.5525 (OUTLIER) cc_final: 0.4566 (p) REVERT: X 59 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: X 117 TRP cc_start: 0.7987 (m-10) cc_final: 0.7609 (m-10) REVERT: Z 24 ASN cc_start: 0.8698 (t0) cc_final: 0.8378 (t0) REVERT: Z 50 MET cc_start: 0.8469 (tpp) cc_final: 0.8165 (mmm) REVERT: Z 133 MET cc_start: 0.8235 (ttp) cc_final: 0.7891 (tpp) REVERT: a 12 MET cc_start: 0.8852 (ttm) cc_final: 0.8409 (ttm) REVERT: a 35 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8297 (mt-10) REVERT: a 43 TYR cc_start: 0.8843 (t80) cc_final: 0.6260 (m-80) REVERT: a 59 ARG cc_start: 0.7279 (ppt170) cc_final: 0.6579 (ppt170) REVERT: b 10 LYS cc_start: 0.7464 (ttmt) cc_final: 0.6966 (ptmm) REVERT: b 18 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8421 (p) REVERT: b 34 MET cc_start: 0.7949 (mtt) cc_final: 0.7659 (mtt) REVERT: q 89 TRP cc_start: 0.8458 (t60) cc_final: 0.8203 (t60) REVERT: r 93 LYS cc_start: 0.8642 (mmmm) cc_final: 0.8271 (mmmm) REVERT: r 101 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7865 (ptm) outliers start: 162 outliers final: 90 residues processed: 964 average time/residue: 0.2098 time to fit residues: 333.2671 Evaluate side-chains 877 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 773 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 123 ASN Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 489 ILE Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 669 SER Chi-restraints excluded: chain G residue 699 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 118 LYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain Q residue 157 SER Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain V residue 96 LYS Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 144 SER Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 101 MET Chi-restraints excluded: chain s residue 42 THR Chi-restraints excluded: chain s residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 223 optimal weight: 3.9990 chunk 391 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 258 optimal weight: 1.9990 chunk 376 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 340 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN P 219 ASN Q 141 ASN S 25 GLN Z 85 GLN ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.120883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091952 restraints weight = 67757.971| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.68 r_work: 0.3164 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 34766 Z= 0.199 Angle : 0.899 73.053 47147 Z= 0.358 Chirality : 0.046 0.208 5143 Planarity : 0.005 0.126 5975 Dihedral : 8.983 139.388 4858 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.83 % Rotamer: Outliers : 4.27 % Allowed : 19.39 % Favored : 76.34 % 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: -0.38 (0.13), residues: 4131 helix: 0.63 (0.12), residues: 1862 sheet: -1.02 (0.26), residues: 377 loop : -0.93 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG X 135 TYR 0.033 0.002 TYR B 170 PHE 0.034 0.002 PHE T 126 TRP 0.018 0.001 TRP F 75 HIS 0.015 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (34726) covalent geometry : angle 0.69786 / 0.35 (47057) SS BOND : bond 0.00524 / 0.26 ( 3) SS BOND : angle 2.78806 / 1.14 ( 6) hydrogen bonds : bond 0.04553 / 2.98 ( 1428) hydrogen bonds : angle 5.19453 / 3.68 ( 4137) metal coordination : bond 0.02435 / 1.61 ( 37) metal coordination : angle 13.41211 / 9.64 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 836 time to evaluate : 1.302 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: B 181 CYS cc_start: 0.8590 (p) cc_final: 0.8216 (p) REVERT: C 168 GLU cc_start: 0.8629 (tm-30) cc_final: 0.7965 (tm-30) REVERT: D 105 MET cc_start: 0.7631 (tpp) cc_final: 0.7249 (tpp) REVERT: D 145 MET cc_start: 0.8572 (mtt) cc_final: 0.8238 (mtt) REVERT: D 215 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8512 (tm-30) REVERT: D 263 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.8877 (m) REVERT: D 359 ASP cc_start: 0.8547 (t0) cc_final: 0.8346 (t0) REVERT: E 69 TYR cc_start: 0.7739 (m-80) cc_final: 0.7244 (m-80) REVERT: E 105 GLN cc_start: 0.8332 (mp10) cc_final: 0.8020 (mp10) REVERT: E 181 ASN cc_start: 0.8167 (m-40) cc_final: 0.7516 (m-40) REVERT: E 192 TYR cc_start: 0.8383 (m-80) cc_final: 0.7983 (m-80) REVERT: E 205 ASP cc_start: 0.8452 (m-30) cc_final: 0.7818 (p0) REVERT: E 242 PHE cc_start: 0.7833 (t80) cc_final: 0.7579 (t80) REVERT: F 102 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7353 (ttp) REVERT: F 191 TYR cc_start: 0.5525 (t80) cc_final: 0.5054 (t80) REVERT: F 248 VAL cc_start: 0.8960 (t) cc_final: 0.8692 (p) REVERT: F 383 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8985 (p) REVERT: F 433 TRP cc_start: 0.8736 (m-10) cc_final: 0.8452 (m-10) REVERT: G 138 ASP cc_start: 0.8646 (m-30) cc_final: 0.8340 (t0) REVERT: G 265 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8843 (t) REVERT: G 364 ASP cc_start: 0.7797 (m-30) cc_final: 0.7257 (t70) REVERT: G 367 CYS cc_start: 0.8326 (m) cc_final: 0.8111 (m) REVERT: G 473 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7968 (ttm) REVERT: G 476 LEU cc_start: 0.9396 (tp) cc_final: 0.9145 (tp) REVERT: G 579 MET cc_start: 0.8629 (ptp) cc_final: 0.8066 (ppp) REVERT: H 56 PHE cc_start: 0.9028 (m-10) cc_final: 0.8776 (m-80) REVERT: H 152 SER cc_start: 0.9333 (m) cc_final: 0.9034 (t) REVERT: H 282 TYR cc_start: 0.8277 (t80) cc_final: 0.7795 (t80) REVERT: I 51 LYS cc_start: 0.8318 (tppt) cc_final: 0.8017 (mmpt) REVERT: I 70 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8884 (mp) REVERT: I 94 SER cc_start: 0.9521 (p) cc_final: 0.8779 (p) REVERT: I 208 ASP cc_start: 0.8498 (t0) cc_final: 0.7916 (t70) REVERT: P 91 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8751 (tp) REVERT: P 118 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8367 (tttp) REVERT: P 205 ASP cc_start: 0.8455 (p0) cc_final: 0.7906 (p0) REVERT: P 211 ASP cc_start: 0.8047 (p0) cc_final: 0.7545 (p0) REVERT: P 215 ASN cc_start: 0.8414 (m-40) cc_final: 0.7920 (m110) REVERT: P 283 MET cc_start: 0.7233 (tpp) cc_final: 0.6972 (tpp) REVERT: P 338 LEU cc_start: 0.8157 (mt) cc_final: 0.7955 (mt) REVERT: P 350 ILE cc_start: 0.8943 (tt) cc_final: 0.8737 (mt) REVERT: P 376 ASN cc_start: 0.6149 (t0) cc_final: 0.5384 (m-40) REVERT: P 377 TYR cc_start: 0.6001 (t80) cc_final: 0.5181 (t80) REVERT: Q 69 GLU cc_start: 0.8553 (tp30) cc_final: 0.8324 (tp30) REVERT: Q 166 TRP cc_start: 0.5613 (t60) cc_final: 0.4973 (t60) REVERT: S 26 ARG cc_start: 0.8414 (tmm-80) cc_final: 0.8155 (ttp80) REVERT: S 64 LYS cc_start: 0.8505 (mtpp) cc_final: 0.7165 (mtmm) REVERT: S 82 LEU cc_start: 0.8820 (tt) cc_final: 0.8500 (tt) REVERT: T 84 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8683 (mp) REVERT: T 93 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.6453 (pt) REVERT: T 114 ASP cc_start: 0.8749 (m-30) cc_final: 0.8495 (m-30) REVERT: V 76 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8387 (mm-30) REVERT: V 81 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8899 (mp) REVERT: V 94 MET cc_start: 0.8639 (mmm) cc_final: 0.8193 (mpp) REVERT: W 24 PHE cc_start: 0.8785 (m-10) cc_final: 0.8438 (m-10) REVERT: W 37 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7668 (mt-10) REVERT: W 45 GLU cc_start: 0.8433 (tp30) cc_final: 0.8011 (tp30) REVERT: W 48 ASN cc_start: 0.8625 (t0) cc_final: 0.8339 (t0) REVERT: W 60 LYS cc_start: 0.8991 (tptm) cc_final: 0.8650 (pttp) REVERT: W 72 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8636 (ttpp) REVERT: W 94 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8644 (tp40) REVERT: X 16 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7952 (tm-30) REVERT: X 94 MET cc_start: 0.8550 (mtp) cc_final: 0.8299 (mtp) REVERT: Z 24 ASN cc_start: 0.8734 (t0) cc_final: 0.8437 (t0) REVERT: Z 50 MET cc_start: 0.8540 (tpp) cc_final: 0.8212 (mmm) REVERT: Z 133 MET cc_start: 0.8171 (ttp) cc_final: 0.7936 (tpt) REVERT: a 35 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8332 (mt-10) REVERT: a 43 TYR cc_start: 0.8824 (t80) cc_final: 0.6300 (m-80) REVERT: a 59 ARG cc_start: 0.7237 (ppt170) cc_final: 0.6593 (ppt170) REVERT: b 8 PHE cc_start: 0.7763 (p90) cc_final: 0.7491 (p90) REVERT: b 10 LYS cc_start: 0.7335 (ttmt) cc_final: 0.6890 (ptmm) REVERT: b 34 MET cc_start: 0.8000 (mtt) cc_final: 0.7660 (mtt) REVERT: q 132 LYS cc_start: 0.8250 (ttpt) cc_final: 0.8006 (ttpt) REVERT: r 93 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8176 (mmmm) REVERT: r 101 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7938 (ptm) outliers start: 155 outliers final: 96 residues processed: 936 average time/residue: 0.1964 time to fit residues: 301.7268 Evaluate side-chains 865 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 757 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 359 ASN Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 699 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 118 LYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain Q residue 157 SER Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 93 ILE Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain V residue 96 LYS Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 144 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 101 MET Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 367 optimal weight: 0.8980 chunk 365 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 chunk 390 optimal weight: 7.9990 chunk 315 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 341 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 108 GLN B 166 ASN B 172 HIS B 216 GLN D 147 ASN D 233 HIS D 234 GLN D 264 ASN D 285 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 171 ASN ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 HIS V 110 ASN ** X 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 11 ASN b 69 HIS q 72 ASN r 9 GLN r 110 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.124549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095437 restraints weight = 69042.903| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.90 r_work: 0.3197 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34766 Z= 0.167 Angle : 0.873 73.960 47147 Z= 0.342 Chirality : 0.044 0.261 5143 Planarity : 0.005 0.127 5975 Dihedral : 8.811 140.538 4858 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 4.19 % Allowed : 20.33 % Favored : 75.48 % 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: -0.29 (0.13), residues: 4131 helix: 0.72 (0.12), residues: 1862 sheet: -0.99 (0.26), residues: 371 loop : -0.88 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 135 TYR 0.035 0.002 TYR Q 160 PHE 0.029 0.002 PHE E 168 TRP 0.019 0.001 TRP F 75 HIS 0.023 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (34726) covalent geometry : angle 0.67092 / 0.34 (47057) SS BOND : bond 0.00533 / 0.26 ( 3) SS BOND : angle 2.32542 / 0.93 ( 6) hydrogen bonds : bond 0.04292 / 2.81 ( 1428) hydrogen bonds : angle 5.09363 / 3.60 ( 4137) metal coordination : bond 0.01951 / 1.32 ( 37) metal coordination : angle 13.24155 / 9.68 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 830 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 SER cc_start: 0.9418 (p) cc_final: 0.9137 (p) REVERT: C 168 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8008 (tm-30) REVERT: C 178 PHE cc_start: 0.8459 (m-80) cc_final: 0.8211 (m-80) REVERT: D 105 MET cc_start: 0.7701 (tpp) cc_final: 0.7354 (tpp) REVERT: D 145 MET cc_start: 0.8598 (mtt) cc_final: 0.8181 (mtt) REVERT: D 215 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8546 (tm-30) REVERT: D 263 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8816 (m) REVERT: D 292 MET cc_start: 0.9056 (mmm) cc_final: 0.8834 (mmt) REVERT: D 359 ASP cc_start: 0.8593 (t0) cc_final: 0.8341 (t0) REVERT: E 59 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.8052 (t80) REVERT: E 61 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7776 (mtt-85) REVERT: E 69 TYR cc_start: 0.7807 (m-80) cc_final: 0.7358 (m-80) REVERT: E 105 GLN cc_start: 0.8348 (mp10) cc_final: 0.7997 (mp10) REVERT: E 181 ASN cc_start: 0.8190 (m-40) cc_final: 0.7531 (m-40) REVERT: E 192 TYR cc_start: 0.8456 (m-80) cc_final: 0.8002 (m-80) REVERT: E 242 PHE cc_start: 0.7834 (t80) cc_final: 0.7585 (t80) REVERT: F 102 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7433 (ttp) REVERT: F 119 GLU cc_start: 0.8270 (pm20) cc_final: 0.8064 (pm20) REVERT: F 157 TYR cc_start: 0.7731 (t80) cc_final: 0.7478 (t80) REVERT: F 162 PHE cc_start: 0.8162 (m-80) cc_final: 0.7878 (m-80) REVERT: F 191 TYR cc_start: 0.5532 (t80) cc_final: 0.5270 (t80) REVERT: F 337 MET cc_start: 0.8493 (mmm) cc_final: 0.8269 (mmm) REVERT: F 383 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.9054 (p) REVERT: F 390 ASP cc_start: 0.8442 (t0) cc_final: 0.8219 (t70) REVERT: F 433 TRP cc_start: 0.8712 (m-10) cc_final: 0.8448 (m-90) REVERT: G 168 LEU cc_start: 0.8927 (mt) cc_final: 0.8612 (mt) REVERT: G 265 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8843 (t) REVERT: G 306 MET cc_start: 0.9071 (mtm) cc_final: 0.8667 (mtp) REVERT: G 364 ASP cc_start: 0.7851 (m-30) cc_final: 0.7331 (t70) REVERT: G 579 MET cc_start: 0.8466 (ptp) cc_final: 0.8144 (ppp) REVERT: H 56 PHE cc_start: 0.8996 (m-10) cc_final: 0.8696 (m-80) REVERT: H 61 MET cc_start: 0.7210 (tpt) cc_final: 0.6604 (ttm) REVERT: H 246 LEU cc_start: 0.8543 (tp) cc_final: 0.8235 (mt) REVERT: H 282 TYR cc_start: 0.8277 (t80) cc_final: 0.7764 (t80) REVERT: I 40 ASN cc_start: 0.8647 (t0) cc_final: 0.8353 (t0) REVERT: I 76 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7672 (t80) REVERT: I 94 SER cc_start: 0.9523 (p) cc_final: 0.8825 (p) REVERT: I 208 ASP cc_start: 0.8514 (t0) cc_final: 0.7972 (t70) REVERT: P 91 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8778 (tp) REVERT: P 118 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8446 (tttp) REVERT: P 205 ASP cc_start: 0.8485 (p0) cc_final: 0.7792 (p0) REVERT: P 211 ASP cc_start: 0.8119 (p0) cc_final: 0.7629 (p0) REVERT: P 215 ASN cc_start: 0.8464 (m-40) cc_final: 0.8015 (m110) REVERT: P 338 LEU cc_start: 0.8138 (mt) cc_final: 0.7911 (mt) REVERT: P 350 ILE cc_start: 0.9008 (tt) cc_final: 0.8799 (mt) REVERT: P 376 ASN cc_start: 0.6413 (t0) cc_final: 0.5544 (m-40) REVERT: P 377 TYR cc_start: 0.5798 (t80) cc_final: 0.4974 (t80) REVERT: Q 69 GLU cc_start: 0.8576 (tp30) cc_final: 0.8347 (tp30) REVERT: Q 146 ASP cc_start: 0.8630 (p0) cc_final: 0.8365 (p0) REVERT: Q 166 TRP cc_start: 0.5795 (t60) cc_final: 0.5012 (t60) REVERT: S 26 ARG cc_start: 0.8369 (tmm-80) cc_final: 0.8127 (ttp80) REVERT: S 64 LYS cc_start: 0.8598 (mtpp) cc_final: 0.6909 (pttm) REVERT: S 75 LYS cc_start: 0.8941 (tppt) cc_final: 0.8710 (mptt) REVERT: S 89 ARG cc_start: 0.8727 (mtp-110) cc_final: 0.8468 (mmm160) REVERT: T 93 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6728 (pt) REVERT: V 23 ARG cc_start: 0.9020 (tpp-160) cc_final: 0.8775 (tpp80) REVERT: V 44 TYR cc_start: 0.8977 (t80) cc_final: 0.8605 (t80) REVERT: V 76 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8422 (mm-30) REVERT: V 81 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8933 (mp) REVERT: V 94 MET cc_start: 0.8598 (mmm) cc_final: 0.8094 (mpp) REVERT: W 37 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7602 (mt-10) REVERT: W 45 GLU cc_start: 0.8534 (tp30) cc_final: 0.8055 (tp30) REVERT: W 48 ASN cc_start: 0.8688 (t0) cc_final: 0.8242 (t0) REVERT: W 60 LYS cc_start: 0.9014 (tptm) cc_final: 0.8664 (pttp) REVERT: W 94 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8676 (tp40) REVERT: X 16 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7962 (tm-30) REVERT: X 44 MET cc_start: 0.8613 (mmt) cc_final: 0.8083 (tpp) REVERT: X 131 VAL cc_start: 0.8332 (p) cc_final: 0.8081 (m) REVERT: Z 24 ASN cc_start: 0.8750 (t0) cc_final: 0.8442 (t0) REVERT: Z 50 MET cc_start: 0.8461 (tpp) cc_final: 0.8150 (mmm) REVERT: Z 133 MET cc_start: 0.8279 (ttp) cc_final: 0.8077 (tpt) REVERT: a 43 TYR cc_start: 0.8793 (t80) cc_final: 0.6266 (m-80) REVERT: a 59 ARG cc_start: 0.7141 (ppt170) cc_final: 0.6569 (ppt170) REVERT: b 8 PHE cc_start: 0.7596 (p90) cc_final: 0.7379 (p90) REVERT: b 10 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7065 (ptmm) REVERT: q 68 MET cc_start: 0.6267 (tmm) cc_final: 0.5947 (tmm) REVERT: q 132 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7940 (ttpt) REVERT: r 101 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7971 (ptm) REVERT: s 47 ASP cc_start: 0.7730 (m-30) cc_final: 0.7279 (m-30) outliers start: 152 outliers final: 92 residues processed: 922 average time/residue: 0.1987 time to fit residues: 303.2193 Evaluate side-chains 864 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 761 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 699 SER Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 118 LYS Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain T residue 93 ILE Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 144 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 101 MET Chi-restraints excluded: chain s residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 56 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 214 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 chunk 304 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 126 optimal weight: 0.0010 chunk 356 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN E 88 GLN F 116 ASN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN H 169 GLN ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 HIS V 110 ASN X 35 GLN ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.126715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.098375 restraints weight = 68830.614| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.80 r_work: 0.3239 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 34766 Z= 0.136 Angle : 0.846 74.353 47147 Z= 0.332 Chirality : 0.043 0.255 5143 Planarity : 0.005 0.127 5975 Dihedral : 8.645 140.668 4858 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 3.66 % Allowed : 21.52 % Favored : 74.82 % 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: -0.17 (0.13), residues: 4131 helix: 0.84 (0.12), residues: 1862 sheet: -1.01 (0.26), residues: 368 loop : -0.83 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 266 TYR 0.033 0.002 TYR B 170 PHE 0.021 0.001 PHE C 178 TRP 0.021 0.001 TRP F 75 HIS 0.024 0.001 HIS S 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (34726) covalent geometry : angle 0.65381 / 0.33 (47057) SS BOND : bond 0.00291 / 0.15 ( 3) SS BOND : angle 1.80388 / 0.71 ( 6) hydrogen bonds : bond 0.04051 / 2.65 ( 1428) hydrogen bonds : angle 4.99985 / 3.53 ( 4137) metal coordination : bond 0.01405 / 0.97 ( 37) metal coordination : angle 12.74192 / 9.32 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 852 time to evaluate : 1.262 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 190 TYR cc_start: 0.9067 (m-80) cc_final: 0.8659 (m-80) REVERT: C 154 SER cc_start: 0.9381 (p) cc_final: 0.9135 (p) REVERT: C 168 GLU cc_start: 0.8621 (tm-30) cc_final: 0.7960 (tm-30) REVERT: C 178 PHE cc_start: 0.8432 (m-80) cc_final: 0.8129 (m-80) REVERT: D 105 MET cc_start: 0.7677 (tpp) cc_final: 0.7352 (tpp) REVERT: D 145 MET cc_start: 0.8530 (mtt) cc_final: 0.8115 (mtt) REVERT: D 215 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8543 (tm-30) REVERT: D 263 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8730 (m) REVERT: D 359 ASP cc_start: 0.8581 (t0) cc_final: 0.8366 (t0) REVERT: E 40 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7155 (m-70) REVERT: E 59 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8049 (t80) REVERT: E 61 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7856 (mtt-85) REVERT: E 69 TYR cc_start: 0.7759 (m-80) cc_final: 0.7393 (m-80) REVERT: E 105 GLN cc_start: 0.8356 (mp10) cc_final: 0.7956 (mp10) REVERT: E 148 LEU cc_start: 0.9023 (tt) cc_final: 0.8561 (pp) REVERT: E 153 ARG cc_start: 0.8455 (tpp80) cc_final: 0.7944 (ptp-170) REVERT: E 181 ASN cc_start: 0.8120 (m-40) cc_final: 0.7520 (m-40) REVERT: E 192 TYR cc_start: 0.8422 (m-80) cc_final: 0.8101 (m-80) REVERT: E 242 PHE cc_start: 0.7794 (t80) cc_final: 0.7551 (t80) REVERT: F 102 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7380 (ttp) REVERT: F 162 PHE cc_start: 0.8160 (m-80) cc_final: 0.7643 (m-80) REVERT: F 337 MET cc_start: 0.8390 (mmm) cc_final: 0.8086 (mmm) REVERT: F 383 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8954 (p) REVERT: F 390 ASP cc_start: 0.8448 (t0) cc_final: 0.8201 (t70) REVERT: F 414 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7590 (tm-30) REVERT: F 433 TRP cc_start: 0.8714 (m-10) cc_final: 0.8449 (m-90) REVERT: F 451 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8212 (tm-30) REVERT: G 138 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8441 (t0) REVERT: G 168 LEU cc_start: 0.8885 (mt) cc_final: 0.8569 (mt) REVERT: G 265 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8796 (t) REVERT: G 306 MET cc_start: 0.9002 (mtm) cc_final: 0.8498 (mtt) REVERT: G 364 ASP cc_start: 0.7863 (m-30) cc_final: 0.7362 (t70) REVERT: G 569 GLN cc_start: 0.8159 (tp40) cc_final: 0.7706 (tp40) REVERT: G 579 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8174 (ppp) REVERT: G 618 GLU cc_start: 0.7596 (mp0) cc_final: 0.7287 (mt-10) REVERT: H 56 PHE cc_start: 0.8963 (m-10) cc_final: 0.8661 (m-80) REVERT: H 61 MET cc_start: 0.7083 (tpt) cc_final: 0.6604 (ttm) REVERT: H 171 HIS cc_start: 0.7828 (m-70) cc_final: 0.7592 (m-70) REVERT: H 282 TYR cc_start: 0.8135 (t80) cc_final: 0.7729 (t80) REVERT: I 40 ASN cc_start: 0.8552 (t0) cc_final: 0.8315 (t0) REVERT: I 59 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7367 (tmm-80) REVERT: I 70 LEU cc_start: 0.9123 (mp) cc_final: 0.8773 (mp) REVERT: I 76 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7676 (t80) REVERT: I 94 SER cc_start: 0.9489 (p) cc_final: 0.8800 (p) REVERT: I 208 ASP cc_start: 0.8420 (t0) cc_final: 0.7909 (t70) REVERT: P 91 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8802 (tp) REVERT: P 118 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8439 (tttp) REVERT: P 205 ASP cc_start: 0.8442 (p0) cc_final: 0.7756 (p0) REVERT: P 211 ASP cc_start: 0.8096 (p0) cc_final: 0.7588 (p0) REVERT: P 215 ASN cc_start: 0.8542 (m-40) cc_final: 0.8092 (m110) REVERT: P 337 ASP cc_start: 0.8604 (t0) cc_final: 0.8358 (t0) REVERT: P 376 ASN cc_start: 0.6443 (t0) cc_final: 0.5576 (m-40) REVERT: P 377 TYR cc_start: 0.5727 (t80) cc_final: 0.4911 (t80) REVERT: Q 69 GLU cc_start: 0.8613 (tp30) cc_final: 0.7729 (tp30) REVERT: Q 73 LYS cc_start: 0.9059 (ptpt) cc_final: 0.8549 (ptpt) REVERT: Q 166 TRP cc_start: 0.5673 (t60) cc_final: 0.4893 (t60) REVERT: S 64 LYS cc_start: 0.8598 (mtpp) cc_final: 0.6944 (pttm) REVERT: S 89 ARG cc_start: 0.8693 (mtp-110) cc_final: 0.8312 (mmm160) REVERT: V 23 ARG cc_start: 0.9005 (tpp-160) cc_final: 0.8758 (tpp80) REVERT: V 76 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8396 (mm-30) REVERT: V 81 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8893 (mp) REVERT: V 94 MET cc_start: 0.8508 (mmm) cc_final: 0.8091 (mpp) REVERT: W 37 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7612 (mt-10) REVERT: W 45 GLU cc_start: 0.8513 (tp30) cc_final: 0.8023 (tp30) REVERT: W 48 ASN cc_start: 0.8693 (t0) cc_final: 0.8356 (t0) REVERT: W 60 LYS cc_start: 0.9006 (tptm) cc_final: 0.8636 (pttp) REVERT: W 94 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8678 (tp40) REVERT: X 44 MET cc_start: 0.8508 (mmt) cc_final: 0.8229 (mmm) REVERT: X 124 GLN cc_start: 0.7487 (mt0) cc_final: 0.7019 (mm110) REVERT: X 131 VAL cc_start: 0.8316 (p) cc_final: 0.8065 (m) REVERT: Z 24 ASN cc_start: 0.8766 (t0) cc_final: 0.8433 (t0) REVERT: Z 50 MET cc_start: 0.8427 (tpp) cc_final: 0.8191 (mmm) REVERT: Z 133 MET cc_start: 0.8358 (ttp) cc_final: 0.8121 (tpt) REVERT: a 43 TYR cc_start: 0.8763 (t80) cc_final: 0.6438 (m-80) REVERT: a 59 ARG cc_start: 0.7077 (ppt170) cc_final: 0.6638 (ppt170) REVERT: b 8 PHE cc_start: 0.7586 (p90) cc_final: 0.7354 (p90) REVERT: b 10 LYS cc_start: 0.7416 (ttmt) cc_final: 0.7033 (ptmm) REVERT: q 68 MET cc_start: 0.6396 (tmm) cc_final: 0.6102 (tmm) REVERT: q 132 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7956 (ttpt) REVERT: r 93 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8215 (mmmm) outliers start: 133 outliers final: 92 residues processed: 931 average time/residue: 0.2114 time to fit residues: 323.4871 Evaluate side-chains 888 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 784 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 31 LEU 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 138 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 369 GLU Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 579 MET 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 57 MET Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 118 LYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 144 SER Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain s residue 42 THR Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 24 optimal weight: 0.0980 chunk 341 optimal weight: 0.6980 chunk 100 optimal weight: 0.0970 chunk 83 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 373 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 270 ASN D 285 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 HIS P 251 ASN S 48 HIS ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.126228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.097015 restraints weight = 68919.972| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.77 r_work: 0.3244 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 34766 Z= 0.142 Angle : 0.846 74.429 47147 Z= 0.332 Chirality : 0.044 0.348 5143 Planarity : 0.005 0.129 5975 Dihedral : 8.497 140.667 4858 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.83 % Rotamer: Outliers : 3.44 % Allowed : 22.48 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4131 helix: 0.93 (0.12), residues: 1854 sheet: -0.99 (0.26), residues: 377 loop : -0.77 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 40 TYR 0.027 0.002 TYR B 170 PHE 0.019 0.001 PHE E 168 TRP 0.022 0.001 TRP F 75 HIS 0.018 0.001 HIS S 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (34726) covalent geometry : angle 0.65488 / 0.33 (47057) SS BOND : bond 0.00203 / 0.11 ( 3) SS BOND : angle 1.51062 / 0.62 ( 6) hydrogen bonds : bond 0.03956 / 2.59 ( 1428) hydrogen bonds : angle 4.94589 / 3.50 ( 4137) metal coordination : bond 0.01514 / 1.02 ( 37) metal coordination : angle 12.71064 / 9.30 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 824 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 TYR cc_start: 0.9071 (m-80) cc_final: 0.8639 (m-80) REVERT: C 154 SER cc_start: 0.9392 (p) cc_final: 0.9160 (p) REVERT: C 168 GLU cc_start: 0.8683 (tm-30) cc_final: 0.7982 (tm-30) REVERT: C 178 PHE cc_start: 0.8496 (m-80) cc_final: 0.8178 (m-80) REVERT: D 145 MET cc_start: 0.8525 (mtt) cc_final: 0.8115 (mtt) REVERT: D 215 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8483 (tm-30) REVERT: D 263 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8589 (m) REVERT: D 264 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7979 (t0) REVERT: D 359 ASP cc_start: 0.8583 (t0) cc_final: 0.8363 (t0) REVERT: E 40 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7108 (m-70) REVERT: E 59 TYR cc_start: 0.8555 (m-80) cc_final: 0.8164 (m-80) REVERT: E 61 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7940 (mtt-85) REVERT: E 69 TYR cc_start: 0.7693 (m-80) cc_final: 0.7350 (m-80) REVERT: E 105 GLN cc_start: 0.8334 (mp10) cc_final: 0.7932 (mp10) REVERT: E 148 LEU cc_start: 0.8899 (tt) cc_final: 0.8506 (pp) REVERT: E 153 ARG cc_start: 0.8513 (tpp80) cc_final: 0.7866 (ptp-170) REVERT: E 181 ASN cc_start: 0.8068 (m-40) cc_final: 0.7603 (m-40) REVERT: E 192 TYR cc_start: 0.8520 (m-80) cc_final: 0.8109 (m-80) REVERT: E 242 PHE cc_start: 0.7794 (t80) cc_final: 0.7552 (t80) REVERT: F 102 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7359 (ttp) REVERT: F 337 MET cc_start: 0.8397 (mmm) cc_final: 0.8071 (mmm) REVERT: F 383 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8921 (p) REVERT: F 433 TRP cc_start: 0.8709 (m-10) cc_final: 0.8406 (m-90) REVERT: F 451 GLN cc_start: 0.8245 (tm130) cc_final: 0.8027 (tm-30) REVERT: G 168 LEU cc_start: 0.8880 (mt) cc_final: 0.8593 (mt) REVERT: G 265 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8826 (t) REVERT: G 306 MET cc_start: 0.8997 (mtm) cc_final: 0.8686 (mtp) REVERT: G 362 ASP cc_start: 0.7949 (t70) cc_final: 0.7477 (t0) REVERT: G 364 ASP cc_start: 0.7855 (m-30) cc_final: 0.7383 (t70) REVERT: G 569 GLN cc_start: 0.8106 (tp40) cc_final: 0.7799 (tp40) REVERT: G 579 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8210 (ppp) REVERT: H 56 PHE cc_start: 0.8964 (m-10) cc_final: 0.8720 (m-80) REVERT: H 61 MET cc_start: 0.7114 (tpt) cc_final: 0.6660 (ttm) REVERT: H 171 HIS cc_start: 0.7869 (m-70) cc_final: 0.7633 (m-70) REVERT: H 184 MET cc_start: 0.8663 (mtm) cc_final: 0.8049 (mtp) REVERT: H 282 TYR cc_start: 0.8157 (t80) cc_final: 0.7792 (t80) REVERT: I 40 ASN cc_start: 0.8535 (t0) cc_final: 0.8295 (t0) REVERT: I 59 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7379 (tmm-80) REVERT: I 65 GLU cc_start: 0.7380 (pt0) cc_final: 0.7114 (pt0) REVERT: I 70 LEU cc_start: 0.9110 (mp) cc_final: 0.8846 (mp) REVERT: I 76 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7722 (t80) REVERT: I 94 SER cc_start: 0.9471 (p) cc_final: 0.8755 (p) REVERT: I 208 ASP cc_start: 0.8455 (t0) cc_final: 0.7934 (t70) REVERT: P 91 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8737 (tp) REVERT: P 118 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8461 (tttp) REVERT: P 140 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7927 (p0) REVERT: P 164 PHE cc_start: 0.8139 (t80) cc_final: 0.7884 (t80) REVERT: P 205 ASP cc_start: 0.8480 (p0) cc_final: 0.7947 (p0) REVERT: P 211 ASP cc_start: 0.8203 (p0) cc_final: 0.7691 (p0) REVERT: P 215 ASN cc_start: 0.8539 (m-40) cc_final: 0.8078 (m110) REVERT: P 337 ASP cc_start: 0.8663 (t0) cc_final: 0.8385 (t0) REVERT: P 338 LEU cc_start: 0.8089 (mt) cc_final: 0.7624 (mp) REVERT: P 376 ASN cc_start: 0.6627 (t0) cc_final: 0.5774 (m-40) REVERT: Q 69 GLU cc_start: 0.8655 (tp30) cc_final: 0.7702 (tp30) REVERT: Q 73 LYS cc_start: 0.9067 (ptpt) cc_final: 0.8499 (ptpt) REVERT: Q 166 TRP cc_start: 0.5540 (t60) cc_final: 0.4741 (t60) REVERT: S 64 LYS cc_start: 0.8613 (mtpp) cc_final: 0.6950 (pttm) REVERT: S 89 ARG cc_start: 0.8699 (mtp-110) cc_final: 0.8278 (mmm160) REVERT: T 82 ARG cc_start: 0.8533 (mtp180) cc_final: 0.8322 (ptm160) REVERT: V 23 ARG cc_start: 0.8996 (tpp-160) cc_final: 0.8744 (tpp80) REVERT: V 76 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8411 (mm-30) REVERT: V 81 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8882 (mp) REVERT: W 37 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7595 (mt-10) REVERT: W 43 TYR cc_start: 0.9108 (t80) cc_final: 0.8904 (t80) REVERT: W 45 GLU cc_start: 0.8536 (tp30) cc_final: 0.8073 (tp30) REVERT: W 48 ASN cc_start: 0.8785 (t0) cc_final: 0.8394 (t0) REVERT: W 60 LYS cc_start: 0.8974 (tptm) cc_final: 0.8638 (pttp) REVERT: W 72 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8672 (ptpt) REVERT: W 94 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8671 (tp40) REVERT: X 131 VAL cc_start: 0.8283 (p) cc_final: 0.8036 (m) REVERT: Z 24 ASN cc_start: 0.8763 (t0) cc_final: 0.8411 (t0) REVERT: Z 50 MET cc_start: 0.8498 (tpp) cc_final: 0.8237 (mmm) REVERT: a 29 PHE cc_start: 0.8849 (t80) cc_final: 0.8390 (t80) REVERT: a 43 TYR cc_start: 0.8767 (t80) cc_final: 0.6393 (m-80) REVERT: a 59 ARG cc_start: 0.7125 (ppt170) cc_final: 0.6820 (ppt170) REVERT: b 8 PHE cc_start: 0.7472 (p90) cc_final: 0.7265 (p90) REVERT: b 10 LYS cc_start: 0.7433 (ttmt) cc_final: 0.7008 (ptmm) REVERT: q 68 MET cc_start: 0.6333 (tmm) cc_final: 0.6054 (tmm) REVERT: r 93 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8118 (mmmm) REVERT: s 47 ASP cc_start: 0.7716 (m-30) cc_final: 0.7351 (m-30) outliers start: 125 outliers final: 97 residues processed: 898 average time/residue: 0.2082 time to fit residues: 307.1025 Evaluate side-chains 885 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 776 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 56 VAL 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 145 MET Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 579 MET 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 73 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 118 LYS Chi-restraints excluded: chain P residue 129 LEU Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain Q residue 157 SER Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 144 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain s residue 42 THR Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 153 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 395 optimal weight: 0.4980 chunk 372 optimal weight: 2.9990 chunk 359 optimal weight: 0.6980 chunk 216 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 270 ASN D 285 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 ASN ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 11 ASN r 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.124652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.097716 restraints weight = 68316.280| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.62 r_work: 0.3225 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34766 Z= 0.180 Angle : 0.877 75.726 47147 Z= 0.346 Chirality : 0.045 0.225 5143 Planarity : 0.005 0.130 5975 Dihedral : 8.473 141.529 4858 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 3.64 % Allowed : 22.84 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4131 helix: 0.93 (0.12), residues: 1850 sheet: -0.97 (0.26), residues: 374 loop : -0.75 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 294 TYR 0.034 0.002 TYR B 170 PHE 0.020 0.001 PHE E 168 TRP 0.025 0.001 TRP F 75 HIS 0.012 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (34726) covalent geometry : angle 0.68446 / 0.34 (47057) SS BOND : bond 0.00618 / 0.30 ( 3) SS BOND : angle 1.74170 / 0.70 ( 6) hydrogen bonds : bond 0.04064 / 2.64 ( 1428) hydrogen bonds : angle 4.97944 / 3.53 ( 4137) metal coordination : bond 0.02055 / 1.33 ( 37) metal coordination : angle 12.99452 / 9.32 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 803 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 SER cc_start: 0.9397 (p) cc_final: 0.9165 (p) REVERT: C 168 GLU cc_start: 0.8691 (tm-30) cc_final: 0.7959 (tm-30) REVERT: C 178 PHE cc_start: 0.8564 (m-80) cc_final: 0.8196 (m-80) REVERT: D 105 MET cc_start: 0.7726 (tpp) cc_final: 0.7420 (tpp) REVERT: D 145 MET cc_start: 0.8520 (mtt) cc_final: 0.8141 (mtt) REVERT: D 215 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8627 (tm-30) REVERT: D 263 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8635 (m) REVERT: E 59 TYR cc_start: 0.8548 (m-80) cc_final: 0.8183 (m-80) REVERT: E 61 ARG cc_start: 0.8234 (mtt90) cc_final: 0.8028 (mtt-85) REVERT: E 69 TYR cc_start: 0.7703 (m-80) cc_final: 0.7282 (m-80) REVERT: E 105 GLN cc_start: 0.8326 (mp10) cc_final: 0.7889 (mp10) REVERT: E 148 LEU cc_start: 0.8866 (tt) cc_final: 0.8490 (pp) REVERT: E 153 ARG cc_start: 0.8488 (tpp80) cc_final: 0.7883 (ptp-170) REVERT: E 181 ASN cc_start: 0.8227 (m-40) cc_final: 0.7789 (m-40) REVERT: E 184 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7762 (ppp) REVERT: E 186 GLN cc_start: 0.7111 (pt0) cc_final: 0.6757 (pm20) REVERT: E 192 TYR cc_start: 0.8373 (m-80) cc_final: 0.7905 (m-80) REVERT: E 205 ASP cc_start: 0.8399 (m-30) cc_final: 0.7665 (p0) REVERT: E 242 PHE cc_start: 0.7823 (t80) cc_final: 0.7584 (t80) REVERT: F 102 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7333 (ttp) REVERT: F 119 GLU cc_start: 0.8225 (pm20) cc_final: 0.7672 (pm20) REVERT: F 337 MET cc_start: 0.8588 (mmm) cc_final: 0.8231 (mmm) REVERT: F 383 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8980 (p) REVERT: F 433 TRP cc_start: 0.8748 (m-10) cc_final: 0.8446 (m-90) REVERT: F 451 GLN cc_start: 0.8241 (tm130) cc_final: 0.7930 (tm-30) REVERT: G 168 LEU cc_start: 0.8859 (mt) cc_final: 0.8571 (mt) REVERT: G 265 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8814 (t) REVERT: G 306 MET cc_start: 0.9019 (mtm) cc_final: 0.8618 (mtp) REVERT: G 362 ASP cc_start: 0.7914 (t70) cc_final: 0.7519 (t0) REVERT: G 364 ASP cc_start: 0.7879 (m-30) cc_final: 0.7506 (t70) REVERT: G 569 GLN cc_start: 0.8116 (tp40) cc_final: 0.7885 (tp40) REVERT: G 579 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8200 (ppp) REVERT: G 618 GLU cc_start: 0.7612 (mp0) cc_final: 0.7383 (mt-10) REVERT: H 56 PHE cc_start: 0.8967 (m-10) cc_final: 0.8730 (m-80) REVERT: H 61 MET cc_start: 0.7104 (tpt) cc_final: 0.6681 (ttm) REVERT: H 171 HIS cc_start: 0.7871 (m-70) cc_final: 0.7617 (m-70) REVERT: H 184 MET cc_start: 0.8680 (mtm) cc_final: 0.7972 (mtp) REVERT: H 282 TYR cc_start: 0.8251 (t80) cc_final: 0.7857 (t80) REVERT: I 40 ASN cc_start: 0.8604 (t0) cc_final: 0.8383 (t0) REVERT: I 55 ASP cc_start: 0.8495 (t70) cc_final: 0.8120 (m-30) REVERT: I 59 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7445 (tmm-80) REVERT: I 70 LEU cc_start: 0.9192 (mp) cc_final: 0.8884 (mp) REVERT: I 76 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7673 (t80) REVERT: I 94 SER cc_start: 0.9457 (p) cc_final: 0.8724 (p) REVERT: I 178 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8297 (mm-30) REVERT: I 208 ASP cc_start: 0.8534 (t0) cc_final: 0.8080 (t70) REVERT: P 91 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8820 (tp) REVERT: P 118 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8461 (tttp) REVERT: P 164 PHE cc_start: 0.8173 (t80) cc_final: 0.7933 (t80) REVERT: P 205 ASP cc_start: 0.8439 (p0) cc_final: 0.7908 (p0) REVERT: P 211 ASP cc_start: 0.8297 (p0) cc_final: 0.7761 (p0) REVERT: P 215 ASN cc_start: 0.8542 (m-40) cc_final: 0.7608 (m110) REVERT: P 283 MET cc_start: 0.7374 (tpp) cc_final: 0.7019 (tpp) REVERT: P 337 ASP cc_start: 0.8654 (t0) cc_final: 0.8388 (t0) REVERT: P 338 LEU cc_start: 0.8172 (mt) cc_final: 0.7655 (mp) REVERT: P 376 ASN cc_start: 0.6729 (t0) cc_final: 0.5820 (m-40) REVERT: Q 69 GLU cc_start: 0.8658 (tp30) cc_final: 0.8453 (tp30) REVERT: S 64 LYS cc_start: 0.8684 (mtpp) cc_final: 0.7008 (pttm) REVERT: S 89 ARG cc_start: 0.8681 (mtp-110) cc_final: 0.8285 (mmm160) REVERT: T 82 ARG cc_start: 0.8492 (mtp180) cc_final: 0.8241 (ptm160) REVERT: T 129 GLU cc_start: 0.7946 (pp20) cc_final: 0.7724 (pp20) REVERT: V 23 ARG cc_start: 0.8988 (tpp-160) cc_final: 0.8724 (tpp80) REVERT: V 76 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8360 (mm-30) REVERT: V 81 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8878 (mp) REVERT: W 37 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7654 (mt-10) REVERT: W 45 GLU cc_start: 0.8551 (tp30) cc_final: 0.8077 (tp30) REVERT: W 48 ASN cc_start: 0.8778 (t0) cc_final: 0.8323 (t0) REVERT: W 60 LYS cc_start: 0.9021 (tptm) cc_final: 0.8675 (pttp) REVERT: W 94 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8655 (tp40) REVERT: X 131 VAL cc_start: 0.8330 (p) cc_final: 0.8087 (m) REVERT: Z 24 ASN cc_start: 0.8810 (t0) cc_final: 0.8427 (t0) REVERT: Z 50 MET cc_start: 0.8551 (tpp) cc_final: 0.8273 (mmm) REVERT: a 29 PHE cc_start: 0.8841 (t80) cc_final: 0.8414 (t80) REVERT: a 43 TYR cc_start: 0.8803 (t80) cc_final: 0.6367 (m-80) REVERT: a 59 ARG cc_start: 0.7251 (ppt170) cc_final: 0.6746 (ppt170) REVERT: b 10 LYS cc_start: 0.7546 (ttmt) cc_final: 0.7103 (ptmm) REVERT: q 68 MET cc_start: 0.6403 (tmm) cc_final: 0.6099 (tmm) REVERT: q 132 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7819 (ttpt) REVERT: r 93 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8127 (mmmm) REVERT: s 47 ASP cc_start: 0.7742 (m-30) cc_final: 0.7318 (m-30) outliers start: 132 outliers final: 95 residues processed: 878 average time/residue: 0.2113 time to fit residues: 305.9647 Evaluate side-chains 875 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 770 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 579 MET Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 701 SER Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 253 GLU 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 139 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 118 LYS Chi-restraints excluded: chain P residue 129 LEU Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain Q residue 157 SER Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 144 SER Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain s residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 44 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 391 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 chunk 342 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 ASN C 180 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 285 ASN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.124865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096995 restraints weight = 68095.257| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.72 r_work: 0.3267 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34766 Z= 0.163 Angle : 0.883 75.437 47147 Z= 0.346 Chirality : 0.045 0.512 5143 Planarity : 0.005 0.131 5975 Dihedral : 8.410 142.376 4858 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 3.28 % Allowed : 23.25 % Favored : 73.47 % 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: -0.01 (0.13), residues: 4131 helix: 0.98 (0.12), residues: 1853 sheet: -0.93 (0.26), residues: 371 loop : -0.75 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 40 TYR 0.031 0.002 TYR B 170 PHE 0.019 0.002 PHE E 168 TRP 0.026 0.001 TRP F 75 HIS 0.017 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (34726) covalent geometry : angle 0.68747 / 0.34 (47057) SS BOND : bond 0.00341 / 0.17 ( 3) SS BOND : angle 1.61818 / 0.65 ( 6) hydrogen bonds : bond 0.04013 / 2.61 ( 1428) hydrogen bonds : angle 4.94082 / 3.49 ( 4137) metal coordination : bond 0.01816 / 1.20 ( 37) metal coordination : angle 13.14533 / 9.41 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 802 time to evaluate : 1.301 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 108 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7253 (mp10) REVERT: C 154 SER cc_start: 0.9348 (p) cc_final: 0.9125 (p) REVERT: C 168 GLU cc_start: 0.8654 (tm-30) cc_final: 0.7927 (tm-30) REVERT: C 178 PHE cc_start: 0.8582 (m-80) cc_final: 0.8140 (m-10) REVERT: D 105 MET cc_start: 0.7718 (tpp) cc_final: 0.7445 (tpp) REVERT: D 145 MET cc_start: 0.8486 (mtt) cc_final: 0.8100 (mtt) REVERT: D 215 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8611 (tm-30) REVERT: D 263 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8658 (m) REVERT: E 59 TYR cc_start: 0.8531 (m-80) cc_final: 0.8182 (m-80) REVERT: E 69 TYR cc_start: 0.7679 (m-80) cc_final: 0.7264 (m-80) REVERT: E 105 GLN cc_start: 0.8386 (mp10) cc_final: 0.8002 (mp10) REVERT: E 148 LEU cc_start: 0.8872 (tt) cc_final: 0.8491 (pp) REVERT: E 153 ARG cc_start: 0.8491 (tpp80) cc_final: 0.7901 (ptp-170) REVERT: E 181 ASN cc_start: 0.8247 (m-40) cc_final: 0.7884 (m-40) REVERT: E 205 ASP cc_start: 0.8382 (m-30) cc_final: 0.7647 (p0) REVERT: E 242 PHE cc_start: 0.7823 (t80) cc_final: 0.7594 (t80) REVERT: F 102 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7293 (ttp) REVERT: F 119 GLU cc_start: 0.8199 (pm20) cc_final: 0.7663 (pm20) REVERT: F 337 MET cc_start: 0.8616 (mmm) cc_final: 0.8283 (mmm) REVERT: F 383 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8947 (p) REVERT: F 433 TRP cc_start: 0.8748 (m-10) cc_final: 0.8463 (m-90) REVERT: F 451 GLN cc_start: 0.8225 (tm130) cc_final: 0.7916 (tm-30) REVERT: G 168 LEU cc_start: 0.8830 (mt) cc_final: 0.8566 (mt) REVERT: G 265 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8806 (t) REVERT: G 306 MET cc_start: 0.8971 (mtm) cc_final: 0.8633 (mtp) REVERT: G 362 ASP cc_start: 0.7865 (t70) cc_final: 0.7436 (t0) REVERT: G 364 ASP cc_start: 0.7835 (m-30) cc_final: 0.7413 (t70) REVERT: G 515 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8637 (pt) REVERT: G 579 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8180 (ppp) REVERT: H 56 PHE cc_start: 0.8955 (m-10) cc_final: 0.8745 (m-80) REVERT: H 61 MET cc_start: 0.7094 (tpt) cc_final: 0.6757 (ttm) REVERT: H 126 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8543 (mmtm) REVERT: H 171 HIS cc_start: 0.7849 (m-70) cc_final: 0.7611 (m-70) REVERT: H 282 TYR cc_start: 0.8226 (t80) cc_final: 0.7785 (t80) REVERT: I 55 ASP cc_start: 0.8527 (t70) cc_final: 0.8169 (m-30) REVERT: I 59 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7451 (tmm-80) REVERT: I 70 LEU cc_start: 0.9200 (mp) cc_final: 0.8922 (mp) REVERT: I 76 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7748 (t80) REVERT: I 94 SER cc_start: 0.9460 (p) cc_final: 0.8738 (p) REVERT: I 208 ASP cc_start: 0.8518 (t0) cc_final: 0.8100 (t70) REVERT: P 91 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8806 (tp) REVERT: P 97 MET cc_start: 0.7845 (ptp) cc_final: 0.7587 (ptp) REVERT: P 118 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8394 (tttp) REVERT: P 121 GLN cc_start: 0.9123 (tt0) cc_final: 0.8739 (pt0) REVERT: P 164 PHE cc_start: 0.8153 (t80) cc_final: 0.7938 (t80) REVERT: P 205 ASP cc_start: 0.8393 (p0) cc_final: 0.7835 (p0) REVERT: P 211 ASP cc_start: 0.8188 (p0) cc_final: 0.7809 (p0) REVERT: P 215 ASN cc_start: 0.8194 (m-40) cc_final: 0.7714 (m110) REVERT: P 338 LEU cc_start: 0.8209 (mt) cc_final: 0.7699 (mp) REVERT: P 376 ASN cc_start: 0.6769 (t0) cc_final: 0.5845 (m-40) REVERT: Q 157 SER cc_start: 0.9350 (t) cc_final: 0.9149 (m) REVERT: S 64 LYS cc_start: 0.8752 (mtpp) cc_final: 0.7099 (pttm) REVERT: S 89 ARG cc_start: 0.8623 (mtp-110) cc_final: 0.8275 (mmm160) REVERT: T 129 GLU cc_start: 0.8030 (pp20) cc_final: 0.7659 (pp20) REVERT: T 131 PRO cc_start: 0.7577 (Cg_endo) cc_final: 0.7326 (Cg_exo) REVERT: V 23 ARG cc_start: 0.9002 (tpp-160) cc_final: 0.8738 (tpp80) REVERT: V 76 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8351 (mm-30) REVERT: V 81 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8920 (mp) REVERT: W 37 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7680 (mt-10) REVERT: W 45 GLU cc_start: 0.8541 (tp30) cc_final: 0.7730 (tp30) REVERT: W 48 ASN cc_start: 0.8835 (t0) cc_final: 0.8305 (t0) REVERT: W 60 LYS cc_start: 0.8982 (tptm) cc_final: 0.8647 (pttp) REVERT: W 94 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8696 (tp40) REVERT: X 50 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7529 (mt-10) REVERT: X 131 VAL cc_start: 0.8296 (p) cc_final: 0.8090 (m) REVERT: Z 24 ASN cc_start: 0.8769 (t0) cc_final: 0.8400 (t0) REVERT: Z 50 MET cc_start: 0.8457 (tpp) cc_final: 0.8241 (mmm) REVERT: a 29 PHE cc_start: 0.8832 (t80) cc_final: 0.8437 (t80) REVERT: a 43 TYR cc_start: 0.8757 (t80) cc_final: 0.6384 (m-80) REVERT: a 59 ARG cc_start: 0.7265 (ppt170) cc_final: 0.6892 (ppt170) REVERT: b 10 LYS cc_start: 0.7551 (ttmt) cc_final: 0.7087 (ptmm) REVERT: q 68 MET cc_start: 0.6398 (tmm) cc_final: 0.6090 (tmm) REVERT: q 132 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7838 (ttpt) REVERT: r 93 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8140 (mmmm) REVERT: s 47 ASP cc_start: 0.7841 (m-30) cc_final: 0.7418 (m-30) outliers start: 119 outliers final: 96 residues processed: 876 average time/residue: 0.2039 time to fit residues: 294.7113 Evaluate side-chains 869 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 763 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 579 MET Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 699 SER Chi-restraints excluded: chain G residue 701 SER Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 253 GLU 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 164 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 118 LYS Chi-restraints excluded: chain P residue 129 LEU Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 53 MET Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 144 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 403 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 301 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN S 25 GLN ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096085 restraints weight = 69530.082| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.10 r_work: 0.3204 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34766 Z= 0.161 Angle : 0.902 76.442 47147 Z= 0.353 Chirality : 0.046 0.871 5143 Planarity : 0.005 0.131 5975 Dihedral : 8.371 142.810 4858 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 3.11 % Allowed : 23.72 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4131 helix: 0.99 (0.12), residues: 1850 sheet: -0.96 (0.26), residues: 371 loop : -0.75 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 40 TYR 0.026 0.002 TYR B 170 PHE 0.023 0.001 PHE G 214 TRP 0.028 0.001 TRP F 75 HIS 0.005 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (34726) covalent geometry : angle 0.70237 / 0.35 (47057) SS BOND : bond 0.00308 / 0.15 ( 3) SS BOND : angle 1.51551 / 0.63 ( 6) hydrogen bonds : bond 0.04021 / 2.61 ( 1428) hydrogen bonds : angle 4.95325 / 3.50 ( 4137) metal coordination : bond 0.01762 / 1.17 ( 37) metal coordination : angle 13.40465 / 9.54 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 806 time to evaluate : 1.357 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 108 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7171 (mp10) REVERT: C 154 SER cc_start: 0.9303 (p) cc_final: 0.9037 (p) REVERT: C 168 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8043 (tm-30) REVERT: C 178 PHE cc_start: 0.8572 (m-80) cc_final: 0.8253 (m-10) REVERT: D 105 MET cc_start: 0.7665 (tpp) cc_final: 0.7365 (tpp) REVERT: D 145 MET cc_start: 0.8548 (mtt) cc_final: 0.8168 (mtt) REVERT: D 215 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8850 (tm-30) REVERT: D 263 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8595 (m) REVERT: D 292 MET cc_start: 0.9134 (mmm) cc_final: 0.8905 (mmt) REVERT: E 59 TYR cc_start: 0.8573 (m-80) cc_final: 0.8241 (m-80) REVERT: E 69 TYR cc_start: 0.7758 (m-80) cc_final: 0.7271 (m-80) REVERT: E 105 GLN cc_start: 0.8404 (mp10) cc_final: 0.8012 (mp10) REVERT: E 148 LEU cc_start: 0.8867 (tt) cc_final: 0.8485 (pp) REVERT: E 153 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7892 (ptp-170) REVERT: E 181 ASN cc_start: 0.8303 (m-40) cc_final: 0.7912 (m-40) REVERT: E 187 ILE cc_start: 0.8020 (mp) cc_final: 0.7756 (mm) REVERT: E 205 ASP cc_start: 0.8376 (m-30) cc_final: 0.7633 (p0) REVERT: E 242 PHE cc_start: 0.7806 (t80) cc_final: 0.7562 (t80) REVERT: F 102 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7191 (ttp) REVERT: F 119 GLU cc_start: 0.8198 (pm20) cc_final: 0.7653 (pm20) REVERT: F 337 MET cc_start: 0.8615 (mmm) cc_final: 0.8292 (mmm) REVERT: F 433 TRP cc_start: 0.8798 (m-10) cc_final: 0.8466 (m-90) REVERT: F 451 GLN cc_start: 0.8313 (tm130) cc_final: 0.8046 (tm-30) REVERT: G 168 LEU cc_start: 0.8859 (mt) cc_final: 0.8645 (mt) REVERT: G 265 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8799 (t) REVERT: G 306 MET cc_start: 0.9030 (mtm) cc_final: 0.8650 (mtp) REVERT: G 362 ASP cc_start: 0.7907 (t70) cc_final: 0.7480 (t0) REVERT: G 364 ASP cc_start: 0.7921 (m-30) cc_final: 0.7543 (t70) REVERT: G 515 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8616 (pt) REVERT: G 579 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8190 (ppp) REVERT: H 61 MET cc_start: 0.7012 (tpt) cc_final: 0.6776 (ttm) REVERT: H 126 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8674 (mmtm) REVERT: H 171 HIS cc_start: 0.7942 (m-70) cc_final: 0.7664 (m-70) REVERT: H 282 TYR cc_start: 0.8276 (t80) cc_final: 0.7968 (t80) REVERT: I 55 ASP cc_start: 0.8562 (t70) cc_final: 0.8175 (m-30) REVERT: I 70 LEU cc_start: 0.9137 (mp) cc_final: 0.8865 (mp) REVERT: I 76 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7800 (t80) REVERT: I 94 SER cc_start: 0.9477 (p) cc_final: 0.8826 (p) REVERT: I 208 ASP cc_start: 0.8641 (t0) cc_final: 0.8199 (t70) REVERT: P 91 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8822 (tp) REVERT: P 97 MET cc_start: 0.8017 (ptp) cc_final: 0.7767 (ptp) REVERT: P 118 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8400 (tttp) REVERT: P 121 GLN cc_start: 0.9091 (tt0) cc_final: 0.8767 (pt0) REVERT: P 164 PHE cc_start: 0.8192 (t80) cc_final: 0.7909 (t80) REVERT: P 205 ASP cc_start: 0.8407 (p0) cc_final: 0.7791 (p0) REVERT: P 211 ASP cc_start: 0.8243 (p0) cc_final: 0.7838 (p0) REVERT: P 215 ASN cc_start: 0.8197 (m-40) cc_final: 0.7719 (m110) REVERT: P 251 ASN cc_start: 0.8320 (m110) cc_final: 0.8057 (m110) REVERT: P 376 ASN cc_start: 0.6757 (t0) cc_final: 0.5819 (m-40) REVERT: Q 157 SER cc_start: 0.9373 (t) cc_final: 0.9166 (m) REVERT: S 64 LYS cc_start: 0.8741 (mtpp) cc_final: 0.7080 (pttm) REVERT: S 89 ARG cc_start: 0.8683 (mtp-110) cc_final: 0.8289 (mmm160) REVERT: T 82 ARG cc_start: 0.8522 (ptm160) cc_final: 0.8300 (ptm160) REVERT: T 92 LYS cc_start: 0.6810 (pttm) cc_final: 0.6481 (pttm) REVERT: V 23 ARG cc_start: 0.8966 (tpp-160) cc_final: 0.8701 (tpp80) REVERT: V 29 THR cc_start: 0.8843 (m) cc_final: 0.8514 (p) REVERT: V 76 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8396 (mm-30) REVERT: V 81 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8902 (mp) REVERT: W 37 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7698 (mt-10) REVERT: W 45 GLU cc_start: 0.8558 (tp30) cc_final: 0.7757 (tp30) REVERT: W 48 ASN cc_start: 0.8809 (t0) cc_final: 0.8283 (t0) REVERT: W 60 LYS cc_start: 0.9010 (tptm) cc_final: 0.8675 (pttp) REVERT: W 94 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8710 (tp40) REVERT: X 131 VAL cc_start: 0.8295 (p) cc_final: 0.8077 (m) REVERT: Z 24 ASN cc_start: 0.8823 (t0) cc_final: 0.8431 (t0) REVERT: Z 50 MET cc_start: 0.8610 (tpp) cc_final: 0.8368 (mmm) REVERT: Z 76 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8295 (tp-100) REVERT: a 29 PHE cc_start: 0.8921 (t80) cc_final: 0.8621 (t80) REVERT: a 43 TYR cc_start: 0.8779 (t80) cc_final: 0.6381 (m-80) REVERT: a 59 ARG cc_start: 0.7248 (ppt170) cc_final: 0.6884 (ppt170) REVERT: b 10 LYS cc_start: 0.7361 (ttmt) cc_final: 0.6926 (tttm) REVERT: q 68 MET cc_start: 0.6228 (tmm) cc_final: 0.5949 (tmm) REVERT: s 47 ASP cc_start: 0.7790 (m-30) cc_final: 0.7301 (m-30) outliers start: 113 outliers final: 91 residues processed: 874 average time/residue: 0.1980 time to fit residues: 284.3212 Evaluate side-chains 865 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 765 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 359 ASN Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 579 MET Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 699 SER Chi-restraints excluded: chain G residue 701 SER Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 253 GLU 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 164 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 118 LYS Chi-restraints excluded: chain P residue 129 LEU Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 53 MET Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 144 SER Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 73 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 329 optimal weight: 0.0970 chunk 175 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 209 optimal weight: 0.1980 chunk 246 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN G 705 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN P 323 HIS ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 GLN Z 85 GLN b 11 ASN r 110 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.125538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097481 restraints weight = 68990.392| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.89 r_work: 0.3245 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 34766 Z= 0.154 Angle : 0.899 76.310 47147 Z= 0.351 Chirality : 0.045 0.626 5143 Planarity : 0.005 0.131 5975 Dihedral : 8.315 142.908 4858 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 3.03 % Allowed : 23.91 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.13), residues: 4131 helix: 1.00 (0.12), residues: 1850 sheet: -1.01 (0.26), residues: 373 loop : -0.74 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 207 TYR 0.030 0.002 TYR V 44 PHE 0.019 0.001 PHE A 92 TRP 0.029 0.001 TRP F 75 HIS 0.010 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (34726) covalent geometry : angle 0.70085 / 0.35 (47057) SS BOND : bond 0.00254 / 0.13 ( 3) SS BOND : angle 1.40218 / 0.59 ( 6) hydrogen bonds : bond 0.03966 / 2.58 ( 1428) hydrogen bonds : angle 4.93496 / 3.49 ( 4137) metal coordination : bond 0.01621 / 1.11 ( 37) metal coordination : angle 13.36162 / 9.53 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9715.99 seconds wall clock time: 167 minutes 4.30 seconds (10024.30 seconds total)