Starting phenix.real_space_refine on Tue May 5 22:22:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xno_38509/05_2026/8xno_38509_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xno_38509/05_2026/8xno_38509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xno_38509/05_2026/8xno_38509_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xno_38509/05_2026/8xno_38509_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xno_38509/05_2026/8xno_38509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xno_38509/05_2026/8xno_38509.map" } resolution = 3.4 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= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 13 5.49 5 S 244 5.16 5 C 21718 2.51 5 N 5754 2.21 5 O 6151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33909 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 754 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3079 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 21, 'TRANS': 362} Chain breaks: 1 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: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2500 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 22, 'TRANS': 290} Chain breaks: 2 Chain: "I" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1398 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 1 Chain: "P" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2730 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "q" Number of atoms: 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: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 418 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Chain: "s" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} 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: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 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: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1017 SG CYS B 99 80.413 59.227 106.514 1.00 29.52 S ATOM 1520 SG CYS B 164 77.581 55.878 111.563 1.00 28.96 S ATOM 1750 SG CYS B 194 82.736 55.663 110.835 1.00 29.28 S ATOM 1023 SG CYS B 100 79.071 55.262 105.776 1.00 30.11 S ATOM 7521 SG CYS E 134 139.826 50.814 153.509 1.00 56.01 S ATOM 7555 SG CYS E 139 142.330 52.397 152.752 1.00 56.50 S ATOM 7839 SG CYS E 175 137.474 54.365 156.066 1.00 54.42 S ATOM 7862 SG CYS E 179 140.792 56.004 156.156 1.00 57.95 S ATOM 11392 SG CYS F 425 121.271 60.301 156.016 1.00 45.60 S ATOM 11070 SG CYS F 385 121.301 57.698 150.279 1.00 39.95 S ATOM 11050 SG CYS F 382 117.039 58.960 152.504 1.00 40.29 S ATOM 11031 SG CYS F 379 118.941 54.935 155.462 1.00 43.09 S ATOM 12440 SG CYS G 131 100.762 47.719 139.145 1.00 31.31 S ATOM 12419 SG CYS G 128 102.840 51.440 134.481 1.00 30.26 S ATOM 12480 SG CYS G 137 100.497 53.654 140.448 1.00 33.13 S ATOM 13165 SG CYS G 226 102.257 47.878 147.737 1.00 34.31 S ATOM 12836 SG CYS G 182 105.357 46.279 153.537 1.00 36.31 S ATOM 12812 SG CYS G 179 104.817 51.814 150.882 1.00 35.62 S ATOM 12789 SG CYS G 176 108.218 47.457 148.513 1.00 34.05 S ATOM 11926 SG CYS G 64 106.295 57.875 152.782 1.00 35.53 S ATOM 12012 SG CYS G 75 107.054 59.876 151.080 1.00 36.47 S ATOM 12037 SG CYS G 78 105.992 64.381 153.097 1.00 36.76 S ATOM 12138 SG CYS G 92 105.735 62.540 156.317 1.00 39.04 S ATOM 20128 SG CYS I 123 86.553 50.625 120.047 1.00 27.30 S ATOM 20354 SG CYS I 152 86.339 49.362 114.956 1.00 27.39 S ATOM 20401 SG CYS I 158 91.982 49.501 117.109 1.00 26.60 S ATOM 20380 SG CYS I 155 88.928 53.948 116.676 1.00 27.04 S ATOM 20077 SG CYS I 116 96.287 46.613 127.595 1.00 29.24 S ATOM 20100 SG CYS I 119 91.947 46.271 124.208 1.00 28.85 S ATOM 20058 SG CYS I 113 95.112 41.427 124.418 1.00 28.61 S ATOM 20430 SG CYS I 162 98.074 45.956 122.254 1.00 28.07 S ATOM 24939 SG CYS R 79 111.463 39.183 127.129 1.00 32.60 S ATOM 25115 SG CYS R 104 108.980 37.811 128.581 1.00 32.49 S ATOM 25137 SG CYS R 107 108.345 38.401 125.138 1.00 30.78 S Time building chain proxies: 8.08, per 1000 atoms: 0.24 Number of scatterers: 33909 At special positions: 0 Unit cell: (167.2, 127.6, 203.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 244 16.00 P 13 15.00 O 6151 8.00 N 5754 7.00 C 21718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS X 36 " - pdb=" SG CYS X 66 " distance=2.00 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.03 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.10 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: 3.45 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 303 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 303 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 304 " pdb="FE3 SF4 I 304 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 304 " - pdb=" SG CYS I 162 " pdb="FE1 SF4 I 304 " - pdb=" SG CYS I 116 " pdb="FE2 SF4 I 304 " - pdb=" SG CYS I 119 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7808 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 36 sheets defined 49.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.314A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 106 Processing helix chain 'B' and resid 70 through 89 removed outlier: 3.751A pdb=" N LYS B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.584A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 3.644A 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: 3.589A 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: 3.603A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.320A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.115A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.967A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.297A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.772A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.862A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.892A 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: 3.860A 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: 3.703A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.668A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.530A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.620A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.638A pdb=" N ALA E 76 " --> pdb=" O HIS E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.525A 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: 3.684A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 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: 3.564A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.922A 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: 3.613A 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: 3.831A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.929A pdb=" N GLY F 237 " --> pdb=" O GLY F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.601A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.532A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.872A 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 296 through 303 removed outlier: 3.862A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 4.040A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.546A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.661A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.807A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.348A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.519A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.599A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.775A 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: 3.713A 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 189 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.932A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.820A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.670A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.026A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.007A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.636A 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: 3.522A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.641A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.749A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.575A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 85 removed outlier: 3.613A pdb=" N PHE H 71 " --> pdb=" O SER H 67 " (cutoff:3.500A) Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 100 through 123 removed outlier: 3.687A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.838A pdb=" N PHE H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU H 133 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA H 135 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 3.800A 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 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: 3.864A 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: 5.990A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.803A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.873A pdb=" N HIS P 93 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.105A 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 Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.594A pdb=" N LYS P 189 " --> pdb=" O ALA P 185 " (cutoff:3.500A) removed outlier: 3.660A 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: 4.082A 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 323 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.034A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) 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: 4.200A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.185A 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 45 through 49 Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.650A 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: 3.514A pdb=" N TYR S 41 " --> pdb=" O ILE S 37 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.557A 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: 3.810A 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: 3.626A 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: 3.857A pdb=" N ARG W 33 " --> pdb=" O ASN W 29 " (cutoff:3.500A) removed outlier: 4.462A 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: 3.517A 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 107 Processing helix chain 'W' and resid 120 through 127 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 35 removed outlier: 4.624A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 50 Processing helix chain 'X' and resid 56 through 77 Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.946A 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 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 1 through 3 No H-bonds generated for 'chain 'a' and resid 1 through 3' Processing helix chain 'a' and resid 4 through 27 removed outlier: 4.499A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 6 through 15 removed outlier: 4.398A pdb=" N ALA b 12 " --> pdb=" O PHE b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.759A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.602A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 78 through 82 removed outlier: 3.537A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) 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: 4.626A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 17 Processing helix chain 's' and resid 78 through 88 removed outlier: 3.657A pdb=" N ASP s 86 " --> pdb=" O ASP s 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.278A pdb=" N MET B 93 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 134 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.568A pdb=" N CYS C 86 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.831A pdb=" N GLU C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.981A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA5 Processing sheet with id=AA6, 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=AA7, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.716A pdb=" N MET D 80 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 101 " --> pdb=" O MET D 80 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG D 96 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA9, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.356A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 397 through 401 removed outlier: 3.500A pdb=" N PHE D 407 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 170 through 171 removed outlier: 3.515A pdb=" N TYR E 192 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.442A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.151A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.486A 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=AB5, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.807A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.866A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.314A 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=AC1, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AC2, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.455A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC3, 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: 7.517A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC6, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.407A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.359A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC9, 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=AC9 Processing sheet with id=AD1, first strand: chain 'P' and resid 263 through 264 Processing sheet with id=AD2, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AD3, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'R' and resid 52 through 53 removed outlier: 7.650A pdb=" N GLN R 52 " --> pdb=" O VAL q 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'R' and resid 76 through 78 Processing sheet with id=AD6, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.508A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 53 through 56 removed outlier: 3.672A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 129 through 130 Processing sheet with id=AD9, 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: 6.885A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) 1407 hydrogen bonds defined for protein. 4104 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: 7.01 Time building geometry restraints manager: 4.41 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: 11478 1.37 - 1.59: 22761 1.59 - 1.80: 264 1.80 - 2.02: 132 2.02 - 2.23: 80 Bond restraints: 34715 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.648 0.730 2.00e-02 2.50e+03 1.33e+03 bond pdb=" CB7 CDL q 201 " pdb=" OB8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.10e-02 8.26e+03 1.12e+02 bond pdb=" CA7 CDL q 201 " pdb=" OA8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.449 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.399 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" N VAL F 235 " pdb=" CA VAL F 235 " ideal model delta sigma weight residual 1.459 1.342 0.117 1.26e-02 6.30e+03 8.68e+01 ... (remaining 34710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.67: 46242 6.67 - 13.33: 610 13.33 - 20.00: 167 20.00 - 26.66: 2 26.66 - 33.33: 2 Bond angle restraints: 47023 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 89.10 25.54 1.52e+00 4.33e-01 2.82e+02 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 110.82 96.91 13.91 9.70e-01 1.06e+00 2.06e+02 angle pdb=" N ILE G 251 " pdb=" CA ILE G 251 " pdb=" C ILE G 251 " ideal model delta sigma weight residual 108.17 126.82 -18.65 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 97.30 16.08 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N VAL I 164 " pdb=" CA VAL I 164 " pdb=" C VAL I 164 " ideal model delta sigma weight residual 112.83 100.08 12.75 9.90e-01 1.02e+00 1.66e+02 ... (remaining 47018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.45: 20209 27.45 - 54.89: 657 54.89 - 82.34: 94 82.34 - 109.78: 9 109.78 - 137.23: 3 Dihedral angle restraints: 20972 sinusoidal: 8862 harmonic: 12110 Sorted by residual: dihedral pdb=" C ASP D 140 " pdb=" N ASP D 140 " pdb=" CA ASP D 140 " pdb=" CB ASP D 140 " ideal model delta harmonic sigma weight residual -122.60 -101.20 -21.40 0 2.50e+00 1.60e-01 7.33e+01 dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.51 -68.51 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS X 78 " pdb=" SG CYS X 78 " pdb=" SG CYS X 110 " pdb=" CB CYS X 110 " ideal model delta sinusoidal sigma weight residual 93.00 31.38 61.62 1 1.00e+01 1.00e-02 5.04e+01 ... (remaining 20969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4506 0.183 - 0.366: 552 0.366 - 0.550: 47 0.550 - 0.733: 4 0.733 - 0.916: 24 Chirality restraints: 5133 Sorted by residual: chirality pdb="FE3 SF4 I 304 " pdb=" S1 SF4 I 304 " pdb=" S2 SF4 I 304 " pdb=" S4 SF4 I 304 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb="FE2 SF4 I 303 " pdb=" S1 SF4 I 303 " pdb=" S3 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False 10.55 9.64 0.91 2.00e-01 2.50e+01 2.07e+01 chirality pdb="FE4 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 5130 not shown) Planarity restraints: 5959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 401 " -0.012 2.00e-02 2.50e+03 1.66e-01 8.30e+02 pdb=" C1M UQ9 H 401 " -0.011 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 401 " -0.005 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 401 " 0.032 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 401 " -0.091 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 401 " 0.093 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 401 " -0.021 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " -0.142 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 401 " -0.028 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 401 " 0.200 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 401 " -0.363 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 401 " 0.347 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 H 401 " -0.013 2.00e-02 2.50e+03 1.77e-01 3.92e+02 pdb=" C11 UQ9 H 401 " 0.155 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " 0.211 2.00e-02 2.50e+03 pdb=" C8 UQ9 H 401 " -0.290 2.00e-02 2.50e+03 pdb=" C9 UQ9 H 401 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET H 91 " -0.106 5.00e-02 4.00e+02 1.63e-01 4.26e+01 pdb=" N PRO H 92 " 0.282 5.00e-02 4.00e+02 pdb=" CA PRO H 92 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO H 92 " -0.086 5.00e-02 4.00e+02 ... (remaining 5956 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 76 2.38 - 3.01: 22573 3.01 - 3.64: 52979 3.64 - 4.27: 83050 4.27 - 4.90: 134774 Nonbonded interactions: 293452 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.756 3.040 nonbonded pdb=" O ASP q 76 " pdb=" OD1 ASP q 76 " model vdw 1.904 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 1.979 3.120 ... (remaining 293447 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 40.540 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 1.140 34756 Z= 1.053 Angle : 2.283 52.571 47115 Z= 1.524 Chirality : 0.133 0.916 5133 Planarity : 0.008 0.177 5959 Dihedral : 13.468 137.231 13152 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 44.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.29 % Favored : 93.61 % Rotamer: Outliers : 0.33 % Allowed : 7.93 % Favored : 91.74 % Cbeta Deviations : 1.84 % 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: -2.12 (0.12), residues: 4118 helix: -0.75 (0.11), residues: 1800 sheet: -1.16 (0.27), residues: 360 loop : -2.06 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 333 TYR 0.046 0.003 TYR B 112 PHE 0.070 0.002 PHE B 121 TRP 0.034 0.002 TRP G 285 HIS 0.012 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.01471 (34715) covalent geometry : angle 2.15811 (47023) SS BOND : bond 0.03600 ( 4) SS BOND : angle 5.78184 ( 8) hydrogen bonds : bond 0.24450 ( 1407) hydrogen bonds : angle 8.85700 ( 4104) metal coordination : bond 0.52814 ( 37) metal coordination : angle 17.72310 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1590 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1578 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 PHE cc_start: 0.8154 (t80) cc_final: 0.7840 (t80) REVERT: B 189 ILE cc_start: 0.8723 (mm) cc_final: 0.8516 (mm) REVERT: D 371 MET cc_start: 0.7525 (ptm) cc_final: 0.7175 (ppp) REVERT: D 409 VAL cc_start: 0.8875 (t) cc_final: 0.8605 (p) REVERT: E 89 ASN cc_start: 0.6545 (m-40) cc_final: 0.6218 (m-40) REVERT: F 43 THR cc_start: 0.6468 (p) cc_final: 0.6188 (p) REVERT: G 251 ILE cc_start: 0.9028 (mm) cc_final: 0.8751 (mm) REVERT: I 40 ASN cc_start: 0.8207 (t0) cc_final: 0.7938 (t0) REVERT: I 86 TYR cc_start: 0.7118 (t80) cc_final: 0.6867 (t80) REVERT: I 153 ILE cc_start: 0.9155 (pp) cc_final: 0.8936 (pt) REVERT: I 154 TYR cc_start: 0.8513 (m-80) cc_final: 0.8069 (m-80) REVERT: R 94 ASN cc_start: 0.8085 (t0) cc_final: 0.7641 (t0) REVERT: S 64 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7976 (mtmt) REVERT: T 119 ILE cc_start: 0.9248 (mm) cc_final: 0.8976 (mm) REVERT: T 130 ILE cc_start: 0.8142 (mp) cc_final: 0.7526 (mp) REVERT: Z 111 PHE cc_start: 0.5794 (m-80) cc_final: 0.5223 (m-80) REVERT: a 12 MET cc_start: 0.7084 (mtp) cc_final: 0.6845 (ttm) REVERT: b 32 MET cc_start: 0.7602 (mmm) cc_final: 0.7229 (mmm) outliers start: 12 outliers final: 1 residues processed: 1585 average time/residue: 0.2273 time to fit residues: 566.3877 Evaluate side-chains 1008 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1007 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN B 207 GLN B 209 GLN C 88 HIS C 123 ASN C 180 HIS C 195 HIS D 117 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 381 HIS D 390 GLN E 73 HIS ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS E 152 GLN ** F 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN G 59 GLN G 74 ASN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 GLN ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 HIS ** G 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 571 HIS G 605 GLN H 97 ASN H 169 GLN H 171 HIS H 292 ASN I 85 ASN I 126 GLN I 159 GLN ** I 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 72 HIS ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 171 ASN ** P 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 323 HIS P 341 GLN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 GLN S 48 HIS V 21 HIS V 41 HIS ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 ASN ** W 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 GLN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 77 HIS X 104 GLN X 109 GLN b 11 ASN q 13 GLN q 31 ASN q 54 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 GLN r 25 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.122743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.095105 restraints weight = 73534.558| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.07 r_work: 0.3232 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 34756 Z= 0.220 Angle : 1.028 69.194 47115 Z= 0.437 Chirality : 0.050 0.289 5133 Planarity : 0.007 0.136 5959 Dihedral : 9.924 147.685 4935 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 4.04 % Allowed : 15.84 % Favored : 80.13 % 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: -0.95 (0.13), residues: 4118 helix: 0.26 (0.12), residues: 1870 sheet: -1.13 (0.25), residues: 391 loop : -1.40 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 382 TYR 0.025 0.002 TYR F 191 PHE 0.033 0.002 PHE H 223 TRP 0.024 0.002 TRP G 285 HIS 0.012 0.002 HIS W 51 Details of bonding type rmsd covalent geometry : bond 0.00484 (34715) covalent geometry : angle 0.84227 (47023) SS BOND : bond 0.01461 ( 4) SS BOND : angle 6.28509 ( 8) hydrogen bonds : bond 0.05883 ( 1407) hydrogen bonds : angle 5.72282 ( 4104) metal coordination : bond 0.02228 ( 37) metal coordination : angle 13.87058 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1031 time to evaluate : 1.316 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 8 PHE cc_start: 0.7662 (m-10) cc_final: 0.7419 (t80) REVERT: A 10 ASN cc_start: 0.7974 (t0) cc_final: 0.7356 (t0) REVERT: A 53 MET cc_start: 0.8160 (mmm) cc_final: 0.7925 (mmm) REVERT: B 115 ASP cc_start: 0.9016 (m-30) cc_final: 0.8752 (t0) REVERT: C 166 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8892 (mt-10) REVERT: D 137 ASP cc_start: 0.8515 (m-30) cc_final: 0.7816 (m-30) REVERT: D 144 MET cc_start: 0.8460 (mpp) cc_final: 0.7992 (mpp) REVERT: D 145 MET cc_start: 0.8605 (mtt) cc_final: 0.8401 (mtt) REVERT: D 148 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8048 (mt-10) REVERT: D 194 ILE cc_start: 0.9232 (mm) cc_final: 0.8877 (tt) REVERT: D 215 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8365 (tm-30) REVERT: D 325 ASP cc_start: 0.8245 (p0) cc_final: 0.7926 (p0) REVERT: D 387 GLU cc_start: 0.8512 (tt0) cc_final: 0.8269 (tt0) REVERT: E 87 ARG cc_start: 0.7918 (mmt-90) cc_final: 0.7690 (mmt-90) REVERT: E 88 GLN cc_start: 0.8568 (tp40) cc_final: 0.8346 (tp40) REVERT: E 89 ASN cc_start: 0.7464 (m-40) cc_final: 0.7199 (m-40) REVERT: E 105 GLN cc_start: 0.8758 (mp10) cc_final: 0.8437 (mp10) REVERT: E 142 ARG cc_start: 0.8472 (tpp80) cc_final: 0.8170 (tpp80) REVERT: E 184 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6646 (tmm) REVERT: F 43 THR cc_start: 0.6946 (p) cc_final: 0.6673 (p) REVERT: F 109 ARG cc_start: 0.6204 (mmm160) cc_final: 0.5907 (mtp85) REVERT: F 119 GLU cc_start: 0.7057 (pm20) cc_final: 0.6123 (pm20) REVERT: F 134 ASP cc_start: 0.7842 (t0) cc_final: 0.7424 (t0) REVERT: F 159 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7537 (mtp180) REVERT: F 162 PHE cc_start: 0.7754 (m-80) cc_final: 0.7263 (m-80) REVERT: F 175 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8098 (mm-30) REVERT: F 269 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8655 (mmp80) REVERT: F 315 LEU cc_start: 0.8910 (mt) cc_final: 0.8566 (mt) REVERT: F 452 ARG cc_start: 0.8410 (mmm160) cc_final: 0.8114 (mtp85) REVERT: G 39 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7622 (tm-30) REVERT: G 123 ASN cc_start: 0.9279 (m-40) cc_final: 0.8993 (m-40) REVERT: G 145 MET cc_start: 0.8710 (mmm) cc_final: 0.8253 (mmm) REVERT: G 188 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8245 (mt-10) REVERT: G 239 THR cc_start: 0.8915 (p) cc_final: 0.8598 (t) REVERT: G 288 ASP cc_start: 0.8576 (m-30) cc_final: 0.8348 (m-30) REVERT: G 306 MET cc_start: 0.9022 (mtm) cc_final: 0.8480 (mtm) REVERT: G 362 ASP cc_start: 0.8291 (t70) cc_final: 0.8045 (p0) REVERT: H 31 MET cc_start: 0.9292 (mtp) cc_final: 0.8935 (mtt) REVERT: H 32 GLN cc_start: 0.8900 (pt0) cc_final: 0.8573 (pt0) REVERT: H 53 MET cc_start: 0.8888 (mtm) cc_final: 0.8570 (mtm) REVERT: H 193 THR cc_start: 0.8531 (p) cc_final: 0.8273 (p) REVERT: H 284 GLN cc_start: 0.8720 (mt0) cc_final: 0.7870 (mt0) REVERT: H 286 MET cc_start: 0.8026 (mmt) cc_final: 0.7717 (mmt) REVERT: I 40 ASN cc_start: 0.8910 (t0) cc_final: 0.8634 (t0) REVERT: I 50 MET cc_start: 0.8139 (mmm) cc_final: 0.7837 (mmt) REVERT: I 56 ASN cc_start: 0.8250 (t0) cc_final: 0.7963 (t0) REVERT: I 60 ILE cc_start: 0.8939 (mt) cc_final: 0.8603 (mp) REVERT: I 178 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7828 (tt0) REVERT: I 208 ASP cc_start: 0.8514 (t70) cc_final: 0.8242 (t70) REVERT: P 152 ILE cc_start: 0.8766 (mt) cc_final: 0.8463 (mp) REVERT: P 215 ASN cc_start: 0.8032 (m110) cc_final: 0.7581 (m110) REVERT: P 244 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8221 (t0) REVERT: P 269 ASN cc_start: 0.6532 (p0) cc_final: 0.6308 (p0) REVERT: P 271 TYR cc_start: 0.8419 (m-80) cc_final: 0.8116 (m-80) REVERT: P 335 LEU cc_start: 0.8274 (mt) cc_final: 0.7931 (mt) REVERT: P 348 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8113 (mtpt) REVERT: Q 52 LEU cc_start: 0.8198 (pp) cc_final: 0.7886 (pt) REVERT: Q 85 ASN cc_start: 0.8332 (p0) cc_final: 0.8082 (p0) REVERT: Q 114 TRP cc_start: 0.8615 (m-10) cc_final: 0.8282 (m-10) REVERT: Q 119 ASP cc_start: 0.8681 (t0) cc_final: 0.8419 (t0) REVERT: Q 160 TYR cc_start: 0.7742 (t80) cc_final: 0.7516 (t80) REVERT: Q 164 PHE cc_start: 0.8276 (m-80) cc_final: 0.7937 (m-80) REVERT: Q 165 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8657 (p) REVERT: R 75 ARG cc_start: 0.7072 (mmp80) cc_final: 0.6655 (mmp80) REVERT: R 94 ASN cc_start: 0.8141 (t0) cc_final: 0.7802 (t0) REVERT: R 113 GLN cc_start: 0.4327 (mp10) cc_final: 0.4022 (mp10) REVERT: S 40 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7405 (tpp80) REVERT: S 57 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7239 (tm-30) REVERT: S 64 LYS cc_start: 0.8341 (mtpp) cc_final: 0.7313 (mtmt) REVERT: T 82 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7511 (mmm-85) REVERT: T 111 ASP cc_start: 0.8700 (t0) cc_final: 0.8226 (t0) REVERT: T 123 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7843 (mt-10) REVERT: T 128 PHE cc_start: 0.6887 (t80) cc_final: 0.6516 (t80) REVERT: V 45 ARG cc_start: 0.8667 (ttt90) cc_final: 0.8466 (ttp80) REVERT: V 110 ASN cc_start: 0.7746 (t0) cc_final: 0.7476 (t0) REVERT: W 24 PHE cc_start: 0.8000 (m-10) cc_final: 0.7790 (m-10) REVERT: W 68 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7623 (tm-30) REVERT: W 69 MET cc_start: 0.8763 (mmt) cc_final: 0.8392 (mmp) REVERT: W 127 MET cc_start: 0.8362 (ppp) cc_final: 0.8079 (ppp) REVERT: X 22 SER cc_start: 0.9368 (p) cc_final: 0.9126 (p) REVERT: X 37 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6503 (p0) REVERT: X 44 MET cc_start: 0.9165 (mmm) cc_final: 0.8793 (mmm) REVERT: Z 66 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8335 (mm-30) REVERT: Z 94 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8046 (tm-30) REVERT: Z 111 PHE cc_start: 0.6370 (m-80) cc_final: 0.5572 (m-80) REVERT: Z 133 MET cc_start: 0.8889 (ttm) cc_final: 0.8593 (tpp) REVERT: a 25 TYR cc_start: 0.8624 (m-80) cc_final: 0.8398 (m-10) REVERT: a 51 ASP cc_start: 0.7760 (m-30) cc_final: 0.7286 (m-30) REVERT: a 54 ILE cc_start: 0.8811 (mm) cc_final: 0.8449 (mm) REVERT: b 41 TYR cc_start: 0.8380 (m-80) cc_final: 0.8098 (m-80) REVERT: q 49 TYR cc_start: 0.7235 (m-80) cc_final: 0.6816 (m-80) REVERT: q 132 LYS cc_start: 0.8558 (ptmt) cc_final: 0.8180 (ptmt) REVERT: s 77 THR cc_start: 0.8365 (m) cc_final: 0.7913 (m) outliers start: 146 outliers final: 61 residues processed: 1106 average time/residue: 0.2051 time to fit residues: 369.2528 Evaluate side-chains 908 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 841 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 448 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 58 ARG Chi-restraints excluded: chain F residue 168 ASN Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 636 TYR Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 348 LYS Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 290 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 297 optimal weight: 0.9980 chunk 367 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN B 166 ASN C 130 ASN D 147 ASN D 265 ASN D 442 HIS ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 170 GLN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 HIS G 74 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 495 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN H 169 GLN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 85 ASN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 HIS X 95 GLN a 58 ASN q 52 ASN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.119912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.092160 restraints weight = 73356.744| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.18 r_work: 0.3172 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 34756 Z= 0.193 Angle : 0.945 71.971 47115 Z= 0.381 Chirality : 0.046 0.240 5133 Planarity : 0.006 0.134 5959 Dihedral : 9.545 143.661 4934 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 3.90 % Allowed : 17.94 % Favored : 78.16 % 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: -0.54 (0.13), residues: 4118 helix: 0.62 (0.12), residues: 1866 sheet: -1.22 (0.25), residues: 394 loop : -1.13 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 266 TYR 0.021 0.002 TYR P 89 PHE 0.035 0.002 PHE T 126 TRP 0.016 0.001 TRP P 134 HIS 0.007 0.001 HIS W 51 Details of bonding type rmsd covalent geometry : bond 0.00449 (34715) covalent geometry : angle 0.74582 (47023) SS BOND : bond 0.01968 ( 4) SS BOND : angle 4.71028 ( 8) hydrogen bonds : bond 0.04936 ( 1407) hydrogen bonds : angle 5.23395 ( 4104) metal coordination : bond 0.02110 ( 37) metal coordination : angle 13.67880 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 917 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8190 (t0) cc_final: 0.7547 (t0) REVERT: A 53 MET cc_start: 0.8265 (mmm) cc_final: 0.8058 (mmm) REVERT: B 115 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8801 (t0) REVERT: C 58 SER cc_start: 0.9243 (t) cc_final: 0.9028 (p) REVERT: C 118 VAL cc_start: 0.9504 (OUTLIER) cc_final: 0.9093 (m) REVERT: D 137 ASP cc_start: 0.8632 (m-30) cc_final: 0.7868 (m-30) REVERT: D 144 MET cc_start: 0.8453 (mpp) cc_final: 0.7860 (mpp) REVERT: D 145 MET cc_start: 0.8647 (mtt) cc_final: 0.8411 (mtt) REVERT: D 148 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7891 (mt-10) REVERT: D 208 GLU cc_start: 0.8368 (tp30) cc_final: 0.7998 (tm-30) REVERT: D 443 MET cc_start: 0.8701 (mmm) cc_final: 0.8179 (mmt) REVERT: E 47 ASN cc_start: 0.3649 (p0) cc_final: 0.3433 (p0) REVERT: E 91 TRP cc_start: 0.8319 (t60) cc_final: 0.8103 (t-100) REVERT: E 105 GLN cc_start: 0.8802 (mp10) cc_final: 0.8571 (mp10) REVERT: E 121 TYR cc_start: 0.8745 (m-80) cc_final: 0.8544 (m-80) REVERT: E 158 LYS cc_start: 0.7222 (tppt) cc_final: 0.6964 (tptt) REVERT: F 134 ASP cc_start: 0.7975 (t0) cc_final: 0.7333 (t0) REVERT: F 147 ARG cc_start: 0.7800 (ttt90) cc_final: 0.7405 (ttm-80) REVERT: F 175 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8118 (mm-30) REVERT: F 262 PHE cc_start: 0.8273 (t80) cc_final: 0.7595 (t80) REVERT: F 269 ARG cc_start: 0.8984 (mpt180) cc_final: 0.8729 (mmp80) REVERT: F 315 LEU cc_start: 0.8847 (mt) cc_final: 0.8451 (mt) REVERT: F 332 CYS cc_start: 0.8701 (m) cc_final: 0.8476 (m) REVERT: F 337 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8565 (mmm) REVERT: G 39 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7734 (tm-30) REVERT: G 42 MET cc_start: 0.8435 (tpp) cc_final: 0.8195 (tpp) REVERT: G 188 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8349 (mt-10) REVERT: G 239 THR cc_start: 0.9017 (p) cc_final: 0.8759 (t) REVERT: G 283 GLU cc_start: 0.8119 (pm20) cc_final: 0.7883 (pt0) REVERT: G 306 MET cc_start: 0.9108 (mtm) cc_final: 0.8766 (mtm) REVERT: G 460 HIS cc_start: 0.7689 (t70) cc_final: 0.7392 (t-90) REVERT: G 571 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.7210 (p90) REVERT: H 32 GLN cc_start: 0.8773 (pt0) cc_final: 0.8538 (pt0) REVERT: H 43 TYR cc_start: 0.8616 (m-80) cc_final: 0.8129 (m-80) REVERT: H 79 LEU cc_start: 0.9007 (tp) cc_final: 0.8760 (tt) REVERT: H 261 MET cc_start: 0.8212 (mmt) cc_final: 0.7675 (mmm) REVERT: H 269 THR cc_start: 0.9494 (m) cc_final: 0.9290 (m) REVERT: H 279 ARG cc_start: 0.8709 (mtm110) cc_final: 0.8457 (mtp-110) REVERT: H 284 GLN cc_start: 0.8607 (mt0) cc_final: 0.7829 (mt0) REVERT: H 286 MET cc_start: 0.8226 (mmt) cc_final: 0.7999 (mmt) REVERT: I 40 ASN cc_start: 0.9021 (t0) cc_final: 0.8769 (t0) REVERT: I 178 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7915 (tt0) REVERT: I 208 ASP cc_start: 0.8720 (t70) cc_final: 0.8402 (t70) REVERT: P 102 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: P 152 ILE cc_start: 0.8866 (mt) cc_final: 0.8591 (mp) REVERT: P 209 ARG cc_start: 0.7710 (ptp-170) cc_final: 0.7204 (ptp-170) REVERT: P 210 GLU cc_start: 0.7911 (mp0) cc_final: 0.7653 (mp0) REVERT: P 211 ASP cc_start: 0.6754 (p0) cc_final: 0.6520 (p0) REVERT: P 215 ASN cc_start: 0.8153 (m110) cc_final: 0.7539 (m110) REVERT: P 269 ASN cc_start: 0.6624 (p0) cc_final: 0.6213 (p0) REVERT: P 271 TYR cc_start: 0.8350 (m-80) cc_final: 0.8107 (m-10) REVERT: P 348 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8503 (mmmm) REVERT: Q 69 GLU cc_start: 0.8816 (tp30) cc_final: 0.8543 (tp30) REVERT: Q 85 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8379 (p0) REVERT: Q 96 LYS cc_start: 0.9405 (mttm) cc_final: 0.9190 (mtpp) REVERT: Q 114 TRP cc_start: 0.8808 (m-10) cc_final: 0.8545 (m-10) REVERT: Q 119 ASP cc_start: 0.8560 (t0) cc_final: 0.8233 (t0) REVERT: Q 164 PHE cc_start: 0.8240 (m-80) cc_final: 0.7677 (m-80) REVERT: R 75 ARG cc_start: 0.7320 (mmp80) cc_final: 0.6862 (mmp80) REVERT: R 94 ASN cc_start: 0.8168 (t0) cc_final: 0.7906 (t0) REVERT: R 113 GLN cc_start: 0.4525 (mp10) cc_final: 0.4312 (mp10) REVERT: S 40 ARG cc_start: 0.8171 (tpp-160) cc_final: 0.7633 (tpp80) REVERT: S 57 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7427 (tm-30) REVERT: S 64 LYS cc_start: 0.8484 (mtpp) cc_final: 0.7493 (mtmt) REVERT: T 111 ASP cc_start: 0.8766 (t0) cc_final: 0.8355 (t0) REVERT: T 137 LYS cc_start: 0.8950 (tppt) cc_final: 0.8743 (tppt) REVERT: V 45 ARG cc_start: 0.8707 (ttt90) cc_final: 0.8498 (ttp80) REVERT: V 110 ASN cc_start: 0.7933 (t0) cc_final: 0.7354 (t0) REVERT: W 43 TYR cc_start: 0.9086 (t80) cc_final: 0.8600 (t80) REVERT: W 68 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7761 (tm-30) REVERT: W 69 MET cc_start: 0.8978 (mmt) cc_final: 0.8530 (mmp) REVERT: W 78 ASP cc_start: 0.8183 (t0) cc_final: 0.7924 (t0) REVERT: W 94 GLN cc_start: 0.8634 (mm110) cc_final: 0.8425 (tt0) REVERT: W 127 MET cc_start: 0.8530 (ppp) cc_final: 0.8186 (ppp) REVERT: X 22 SER cc_start: 0.9313 (p) cc_final: 0.8870 (m) REVERT: Z 111 PHE cc_start: 0.6442 (m-80) cc_final: 0.5808 (m-80) REVERT: Z 125 TYR cc_start: 0.8837 (m-80) cc_final: 0.8579 (m-80) REVERT: a 4 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8554 (mm-30) REVERT: a 51 ASP cc_start: 0.7580 (m-30) cc_final: 0.6899 (m-30) REVERT: a 54 ILE cc_start: 0.8875 (mm) cc_final: 0.8574 (mm) REVERT: q 49 TYR cc_start: 0.7445 (m-80) cc_final: 0.6965 (m-80) REVERT: q 93 MET cc_start: 0.7815 (mmm) cc_final: 0.7365 (mmm) REVERT: q 132 LYS cc_start: 0.8561 (ptmt) cc_final: 0.7960 (ptmt) outliers start: 141 outliers final: 77 residues processed: 983 average time/residue: 0.2040 time to fit residues: 327.4076 Evaluate side-chains 903 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 819 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 168 ASN Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 102 GLN Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 348 LYS Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 85 ASN Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 35 LEU 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 18 VAL Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain q residue 20 LEU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 88 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 391 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 296 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 108 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN F 136 HIS F 270 ASN F 436 GLN G 140 GLN G 202 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 ASN ** G 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN H 169 GLN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 52 ASN q 59 HIS ** s 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.118026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090083 restraints weight = 73204.069| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.11 r_work: 0.3137 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 34756 Z= 0.201 Angle : 0.955 74.165 47115 Z= 0.369 Chirality : 0.046 0.271 5133 Planarity : 0.005 0.134 5959 Dihedral : 9.318 137.641 4934 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 4.53 % Allowed : 18.35 % Favored : 77.11 % 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: 4118 helix: 0.69 (0.12), residues: 1881 sheet: -1.07 (0.26), residues: 385 loop : -1.01 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 79 TYR 0.025 0.002 TYR Q 160 PHE 0.033 0.002 PHE T 126 TRP 0.030 0.002 TRP G 100 HIS 0.011 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00472 (34715) covalent geometry : angle 0.72936 (47023) SS BOND : bond 0.02153 ( 4) SS BOND : angle 4.71238 ( 8) hydrogen bonds : bond 0.04571 ( 1407) hydrogen bonds : angle 5.10063 ( 4104) metal coordination : bond 0.02203 ( 37) metal coordination : angle 14.54065 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 867 time to evaluate : 1.281 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: A 10 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7553 (t0) REVERT: A 105 GLU cc_start: 0.9145 (tp30) cc_final: 0.8917 (tp30) REVERT: A 108 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: B 115 ASP cc_start: 0.9292 (OUTLIER) cc_final: 0.8911 (t0) REVERT: B 220 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.9005 (tp) REVERT: C 58 SER cc_start: 0.9237 (t) cc_final: 0.9009 (p) REVERT: C 96 LEU cc_start: 0.9492 (mt) cc_final: 0.9240 (mm) REVERT: C 118 VAL cc_start: 0.9489 (OUTLIER) cc_final: 0.9096 (m) REVERT: C 149 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8270 (pp) REVERT: D 137 ASP cc_start: 0.8703 (m-30) cc_final: 0.7951 (m-30) REVERT: D 144 MET cc_start: 0.8531 (mpp) cc_final: 0.7929 (mpp) REVERT: D 148 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7846 (mt-10) REVERT: D 202 TRP cc_start: 0.9000 (m-10) cc_final: 0.8794 (m-10) REVERT: D 208 GLU cc_start: 0.8314 (tp30) cc_final: 0.7925 (tm-30) REVERT: D 215 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 443 MET cc_start: 0.8869 (mmm) cc_final: 0.8312 (mmt) REVERT: E 158 LYS cc_start: 0.7424 (tppt) cc_final: 0.7213 (tptt) REVERT: E 167 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7733 (tp) REVERT: E 245 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6222 (pp30) REVERT: F 131 MET cc_start: 0.8100 (ttt) cc_final: 0.7745 (tmm) REVERT: F 134 ASP cc_start: 0.8088 (t0) cc_final: 0.7387 (t0) REVERT: F 147 ARG cc_start: 0.7756 (ttt90) cc_final: 0.7404 (ttm-80) REVERT: F 175 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8140 (mm-30) REVERT: F 262 PHE cc_start: 0.8277 (t80) cc_final: 0.7594 (t80) REVERT: F 315 LEU cc_start: 0.8907 (mt) cc_final: 0.8390 (mt) REVERT: F 332 CYS cc_start: 0.8707 (m) cc_final: 0.8465 (m) REVERT: F 337 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8486 (mmm) REVERT: F 436 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6839 (mt0) REVERT: F 442 PHE cc_start: 0.8577 (m-80) cc_final: 0.8227 (m-10) REVERT: G 39 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7679 (tm-30) REVERT: G 239 THR cc_start: 0.9147 (p) cc_final: 0.8923 (t) REVERT: G 284 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7620 (tm-30) REVERT: G 306 MET cc_start: 0.9129 (mtm) cc_final: 0.8708 (mtm) REVERT: G 460 HIS cc_start: 0.7724 (t70) cc_final: 0.7277 (t-90) REVERT: G 571 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.7309 (p90) REVERT: H 5 ASN cc_start: 0.9009 (t0) cc_final: 0.8751 (t0) REVERT: H 32 GLN cc_start: 0.8835 (pt0) cc_final: 0.8507 (pt0) REVERT: H 43 TYR cc_start: 0.8629 (m-80) cc_final: 0.8194 (m-80) REVERT: H 59 GLU cc_start: 0.8318 (tt0) cc_final: 0.8117 (tt0) REVERT: H 68 MET cc_start: 0.7377 (ptt) cc_final: 0.6920 (ptp) REVERT: H 79 LEU cc_start: 0.9073 (tp) cc_final: 0.8804 (tt) REVERT: H 279 ARG cc_start: 0.8667 (mtm110) cc_final: 0.8292 (mtp-110) REVERT: H 284 GLN cc_start: 0.8584 (mt0) cc_final: 0.7832 (mt0) REVERT: I 40 ASN cc_start: 0.9023 (t0) cc_final: 0.8795 (t0) REVERT: I 63 TRP cc_start: 0.9126 (m-10) cc_final: 0.8862 (m-10) REVERT: I 76 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7936 (t80) REVERT: I 208 ASP cc_start: 0.8854 (t70) cc_final: 0.8545 (t70) REVERT: P 102 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: P 152 ILE cc_start: 0.8923 (mt) cc_final: 0.8660 (mp) REVERT: P 209 ARG cc_start: 0.7743 (ptp-170) cc_final: 0.6957 (ptp-170) REVERT: P 210 GLU cc_start: 0.8027 (mp0) cc_final: 0.7748 (mp0) REVERT: P 348 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8513 (mmmt) REVERT: Q 96 LYS cc_start: 0.9431 (mttm) cc_final: 0.9219 (mtpp) REVERT: R 75 ARG cc_start: 0.7370 (mmp80) cc_final: 0.6892 (mmp80) REVERT: R 94 ASN cc_start: 0.8051 (t0) cc_final: 0.7771 (t0) REVERT: S 40 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7563 (tpp80) REVERT: S 57 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7487 (tm-30) REVERT: S 64 LYS cc_start: 0.8521 (mtpp) cc_final: 0.7587 (mtmt) REVERT: T 111 ASP cc_start: 0.8796 (t0) cc_final: 0.8498 (t0) REVERT: T 116 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8188 (p) REVERT: T 117 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8636 (mm-30) REVERT: T 120 MET cc_start: 0.8670 (mtm) cc_final: 0.8223 (mtp) REVERT: T 148 ILE cc_start: 0.7569 (mm) cc_final: 0.6738 (mm) REVERT: V 45 ARG cc_start: 0.8713 (ttt90) cc_final: 0.8484 (ttp80) REVERT: V 110 ASN cc_start: 0.7983 (t0) cc_final: 0.7372 (t0) REVERT: W 68 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7959 (tm-30) REVERT: W 69 MET cc_start: 0.9038 (mmt) cc_final: 0.8645 (mmt) REVERT: W 78 ASP cc_start: 0.8275 (t0) cc_final: 0.7926 (t0) REVERT: W 92 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7870 (mm-30) REVERT: W 127 MET cc_start: 0.8543 (ppp) cc_final: 0.8171 (ppp) REVERT: X 22 SER cc_start: 0.9290 (p) cc_final: 0.8859 (m) REVERT: X 26 LYS cc_start: 0.8637 (tttt) cc_final: 0.8373 (tttt) REVERT: X 44 MET cc_start: 0.9268 (mmm) cc_final: 0.9047 (mmm) REVERT: Z 10 MET cc_start: 0.8390 (tpp) cc_final: 0.8183 (mmt) REVERT: Z 93 GLU cc_start: 0.7358 (tp30) cc_final: 0.7008 (tp30) REVERT: Z 111 PHE cc_start: 0.6817 (m-80) cc_final: 0.6064 (m-80) REVERT: Z 133 MET cc_start: 0.8891 (tpp) cc_final: 0.8646 (tpp) REVERT: a 4 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8530 (mm-30) REVERT: a 46 TYR cc_start: 0.9260 (t80) cc_final: 0.9015 (t80) REVERT: a 51 ASP cc_start: 0.7605 (m-30) cc_final: 0.6931 (m-30) REVERT: a 54 ILE cc_start: 0.8846 (mm) cc_final: 0.8577 (mm) REVERT: b 44 MET cc_start: 0.9090 (mpp) cc_final: 0.8559 (mpp) REVERT: q 49 TYR cc_start: 0.7476 (m-80) cc_final: 0.6998 (m-80) REVERT: q 68 MET cc_start: 0.4050 (OUTLIER) cc_final: 0.3388 (ttt) REVERT: q 81 MET cc_start: 0.7139 (mtt) cc_final: 0.6679 (mtt) REVERT: q 93 MET cc_start: 0.8075 (mmm) cc_final: 0.7846 (mmt) outliers start: 164 outliers final: 98 residues processed: 955 average time/residue: 0.2070 time to fit residues: 323.9689 Evaluate side-chains 913 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 799 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 138 SER 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 235 ASN Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 102 GLN Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 348 LYS Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 92 GLN Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 20 LEU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 68 MET Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 99 optimal weight: 0.3980 chunk 201 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 372 optimal weight: 0.9980 chunk 367 optimal weight: 0.7980 chunk 365 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 108 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 270 ASN F 376 HIS F 436 GLN ** G 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 HIS P 285 HIS Q 92 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN X 143 HIS Z 76 GLN q 52 ASN s 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.093169 restraints weight = 73044.311| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.01 r_work: 0.3217 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 34756 Z= 0.145 Angle : 0.921 74.189 47115 Z= 0.348 Chirality : 0.044 0.213 5133 Planarity : 0.005 0.129 5959 Dihedral : 9.235 143.556 4934 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 3.76 % Allowed : 19.90 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.34 (0.13), residues: 4118 helix: 0.79 (0.12), residues: 1876 sheet: -1.27 (0.25), residues: 407 loop : -0.99 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 266 TYR 0.026 0.002 TYR V 44 PHE 0.029 0.002 PHE T 126 TRP 0.029 0.001 TRP G 100 HIS 0.006 0.001 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00340 (34715) covalent geometry : angle 0.69183 (47023) SS BOND : bond 0.00685 ( 4) SS BOND : angle 4.32606 ( 8) hydrogen bonds : bond 0.04231 ( 1407) hydrogen bonds : angle 4.94054 ( 4104) metal coordination : bond 0.01407 ( 37) metal coordination : angle 14.36405 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 893 time to evaluate : 1.391 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 4 TYR cc_start: 0.8979 (m-80) cc_final: 0.8671 (m-10) REVERT: A 10 ASN cc_start: 0.8127 (t160) cc_final: 0.7517 (t0) REVERT: B 72 GLU cc_start: 0.8825 (tp30) cc_final: 0.8287 (tt0) REVERT: B 95 PHE cc_start: 0.6340 (OUTLIER) cc_final: 0.5227 (m-80) REVERT: B 115 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8856 (t0) REVERT: C 58 SER cc_start: 0.9220 (t) cc_final: 0.9005 (p) REVERT: C 96 LEU cc_start: 0.9449 (mt) cc_final: 0.9201 (mm) REVERT: C 149 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8299 (pp) REVERT: C 214 GLU cc_start: 0.8649 (tt0) cc_final: 0.8288 (tt0) REVERT: C 231 LYS cc_start: 0.9234 (tttt) cc_final: 0.9023 (ptmt) REVERT: D 137 ASP cc_start: 0.8502 (m-30) cc_final: 0.7611 (m-30) REVERT: D 144 MET cc_start: 0.8258 (mpp) cc_final: 0.7839 (mpp) REVERT: D 148 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7835 (mt-10) REVERT: D 202 TRP cc_start: 0.8924 (m-10) cc_final: 0.8696 (m-10) REVERT: D 208 GLU cc_start: 0.8261 (tp30) cc_final: 0.7942 (tm-30) REVERT: D 212 GLU cc_start: 0.8306 (tp30) cc_final: 0.8071 (tp30) REVERT: D 215 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8269 (tm-30) REVERT: D 376 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: D 443 MET cc_start: 0.8605 (mmm) cc_final: 0.8275 (mmt) REVERT: E 39 VAL cc_start: 0.7511 (t) cc_final: 0.7262 (p) REVERT: E 91 TRP cc_start: 0.7672 (t-100) cc_final: 0.7291 (t-100) REVERT: E 184 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6093 (tmm) REVERT: E 245 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6209 (pp30) REVERT: F 101 PHE cc_start: 0.8685 (m-80) cc_final: 0.8313 (m-80) REVERT: F 119 GLU cc_start: 0.6941 (pm20) cc_final: 0.6532 (pm20) REVERT: F 134 ASP cc_start: 0.8054 (t0) cc_final: 0.7342 (t0) REVERT: F 147 ARG cc_start: 0.7815 (ttt90) cc_final: 0.7503 (ttm-80) REVERT: F 158 ILE cc_start: 0.8233 (pt) cc_final: 0.7962 (tt) REVERT: F 175 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8114 (mm-30) REVERT: F 262 PHE cc_start: 0.8325 (t80) cc_final: 0.7731 (t80) REVERT: F 315 LEU cc_start: 0.8932 (mt) cc_final: 0.8483 (mt) REVERT: F 332 CYS cc_start: 0.8640 (m) cc_final: 0.8402 (m) REVERT: F 336 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6583 (pt) REVERT: F 442 PHE cc_start: 0.8617 (m-80) cc_final: 0.8267 (m-10) REVERT: G 39 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7685 (tm-30) REVERT: G 239 THR cc_start: 0.8999 (p) cc_final: 0.8763 (t) REVERT: G 284 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7498 (tm-30) REVERT: G 306 MET cc_start: 0.9072 (mtm) cc_final: 0.8771 (mtm) REVERT: G 496 MET cc_start: 0.9015 (tpp) cc_final: 0.8646 (tmm) REVERT: G 500 ILE cc_start: 0.9249 (mt) cc_final: 0.8930 (mt) REVERT: G 571 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.7329 (p90) REVERT: G 579 MET cc_start: 0.8297 (ptm) cc_final: 0.7987 (tmm) REVERT: H 32 GLN cc_start: 0.8792 (pt0) cc_final: 0.8562 (pt0) REVERT: H 43 TYR cc_start: 0.8620 (m-80) cc_final: 0.8138 (m-80) REVERT: H 59 GLU cc_start: 0.8351 (tt0) cc_final: 0.8128 (tt0) REVERT: H 68 MET cc_start: 0.7373 (ptt) cc_final: 0.6903 (ptp) REVERT: H 108 THR cc_start: 0.9501 (m) cc_final: 0.9209 (p) REVERT: H 152 SER cc_start: 0.9503 (m) cc_final: 0.8856 (t) REVERT: H 265 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8748 (tt) REVERT: H 279 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8270 (mtp-110) REVERT: H 284 GLN cc_start: 0.8554 (mt0) cc_final: 0.7800 (mt0) REVERT: I 70 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9133 (mp) REVERT: I 76 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7920 (t80) REVERT: I 208 ASP cc_start: 0.8846 (t70) cc_final: 0.8565 (t70) REVERT: P 152 ILE cc_start: 0.9007 (mt) cc_final: 0.8764 (mp) REVERT: P 210 GLU cc_start: 0.7980 (mp0) cc_final: 0.7717 (mp0) REVERT: P 271 TYR cc_start: 0.8026 (m-10) cc_final: 0.7777 (m-10) REVERT: P 348 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8594 (mtpt) REVERT: R 75 ARG cc_start: 0.7497 (mmp80) cc_final: 0.6827 (mmp80) REVERT: R 94 ASN cc_start: 0.8004 (t0) cc_final: 0.7619 (t0) REVERT: R 95 LEU cc_start: 0.7405 (mt) cc_final: 0.6762 (mt) REVERT: S 57 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7357 (tm-30) REVERT: S 64 LYS cc_start: 0.8571 (mtpp) cc_final: 0.7644 (mtmt) REVERT: T 82 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.7992 (mmm-85) REVERT: T 97 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7958 (tttt) REVERT: T 111 ASP cc_start: 0.8736 (t0) cc_final: 0.8484 (t0) REVERT: T 117 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8724 (mm-30) REVERT: V 45 ARG cc_start: 0.8706 (ttt90) cc_final: 0.8428 (ttp80) REVERT: V 110 ASN cc_start: 0.7878 (t0) cc_final: 0.7247 (t0) REVERT: W 32 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7993 (mtpt) REVERT: W 68 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8168 (tm-30) REVERT: W 69 MET cc_start: 0.9111 (mmt) cc_final: 0.8779 (mmt) REVERT: W 78 ASP cc_start: 0.8270 (t0) cc_final: 0.7896 (t0) REVERT: W 84 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8810 (tt) REVERT: W 92 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7822 (mm-30) REVERT: W 127 MET cc_start: 0.8450 (ppp) cc_final: 0.8061 (ppp) REVERT: X 22 SER cc_start: 0.9283 (p) cc_final: 0.8890 (m) REVERT: X 44 MET cc_start: 0.9245 (mmm) cc_final: 0.9017 (mmm) REVERT: Z 93 GLU cc_start: 0.7369 (tp30) cc_final: 0.7142 (tp30) REVERT: Z 125 TYR cc_start: 0.8867 (m-80) cc_final: 0.8573 (m-80) REVERT: Z 142 TRP cc_start: 0.8652 (m-10) cc_final: 0.8192 (m-10) REVERT: a 4 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8449 (mm-30) REVERT: a 46 TYR cc_start: 0.9186 (t80) cc_final: 0.8876 (t80) REVERT: a 51 ASP cc_start: 0.7370 (m-30) cc_final: 0.6616 (m-30) REVERT: a 54 ILE cc_start: 0.8738 (mm) cc_final: 0.8482 (mm) REVERT: b 15 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7714 (ptpt) REVERT: b 44 MET cc_start: 0.9090 (mpp) cc_final: 0.8711 (mpp) REVERT: q 49 TYR cc_start: 0.7509 (m-80) cc_final: 0.7023 (m-80) REVERT: q 68 MET cc_start: 0.3962 (OUTLIER) cc_final: 0.3140 (ttt) REVERT: q 81 MET cc_start: 0.7150 (mtt) cc_final: 0.6658 (mtt) outliers start: 136 outliers final: 78 residues processed: 960 average time/residue: 0.2059 time to fit residues: 323.5587 Evaluate side-chains 900 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 807 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 348 LYS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain W residue 32 LYS Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 68 MET Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 62 optimal weight: 0.7980 chunk 279 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 351 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 219 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 GLN Q 92 ASN Q 123 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093744 restraints weight = 73083.088| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.14 r_work: 0.3178 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 34756 Z= 0.143 Angle : 0.915 75.499 47115 Z= 0.344 Chirality : 0.044 0.303 5133 Planarity : 0.005 0.129 5959 Dihedral : 9.093 142.345 4934 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 3.81 % Allowed : 20.87 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4118 helix: 0.80 (0.12), residues: 1872 sheet: -1.21 (0.25), residues: 411 loop : -0.99 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 266 TYR 0.033 0.002 TYR C 63 PHE 0.029 0.002 PHE a 3 TRP 0.029 0.001 TRP P 134 HIS 0.008 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00335 (34715) covalent geometry : angle 0.68986 (47023) SS BOND : bond 0.00488 ( 4) SS BOND : angle 1.15772 ( 8) hydrogen bonds : bond 0.04071 ( 1407) hydrogen bonds : angle 4.87055 ( 4104) metal coordination : bond 0.01486 ( 37) metal coordination : angle 14.25666 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 863 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: 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: 0.8988 (m-80) cc_final: 0.8670 (m-10) REVERT: A 10 ASN cc_start: 0.8204 (t160) cc_final: 0.7545 (t0) REVERT: B 72 GLU cc_start: 0.8832 (tp30) cc_final: 0.8332 (tt0) REVERT: B 95 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5080 (m-80) REVERT: B 107 MET cc_start: 0.8395 (ttp) cc_final: 0.8188 (ttp) REVERT: B 115 ASP cc_start: 0.9249 (OUTLIER) cc_final: 0.8890 (t0) REVERT: B 199 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8174 (mp0) REVERT: B 220 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8896 (tp) REVERT: C 58 SER cc_start: 0.9213 (t) cc_final: 0.8987 (p) REVERT: C 96 LEU cc_start: 0.9432 (mt) cc_final: 0.9181 (mm) REVERT: C 149 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8388 (pp) REVERT: D 137 ASP cc_start: 0.8529 (m-30) cc_final: 0.7642 (m-30) REVERT: D 144 MET cc_start: 0.8212 (mpp) cc_final: 0.7824 (mpp) REVERT: D 148 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7889 (mt-10) REVERT: D 202 TRP cc_start: 0.8952 (m-10) cc_final: 0.8748 (m-10) REVERT: D 208 GLU cc_start: 0.8294 (tp30) cc_final: 0.7965 (tm-30) REVERT: D 212 GLU cc_start: 0.8325 (tp30) cc_final: 0.8094 (tp30) REVERT: D 215 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8382 (tm-30) REVERT: E 39 VAL cc_start: 0.7594 (t) cc_final: 0.7384 (p) REVERT: E 121 TYR cc_start: 0.8846 (m-80) cc_final: 0.8462 (m-80) REVERT: E 167 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8020 (tp) REVERT: E 184 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6529 (tmm) REVERT: E 245 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6201 (pp30) REVERT: F 53 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8324 (mt) REVERT: F 68 ILE cc_start: 0.9212 (mt) cc_final: 0.8916 (tp) REVERT: F 101 PHE cc_start: 0.8675 (m-80) cc_final: 0.8264 (m-80) REVERT: F 134 ASP cc_start: 0.7944 (t0) cc_final: 0.7164 (t0) REVERT: F 147 ARG cc_start: 0.7906 (ttt90) cc_final: 0.7551 (ttm-80) REVERT: F 149 MET cc_start: 0.7654 (mtp) cc_final: 0.7203 (mmp) REVERT: F 191 TYR cc_start: 0.5540 (t80) cc_final: 0.5257 (t80) REVERT: F 262 PHE cc_start: 0.8361 (t80) cc_final: 0.7669 (t80) REVERT: F 315 LEU cc_start: 0.8916 (mt) cc_final: 0.8475 (mt) REVERT: F 332 CYS cc_start: 0.8668 (m) cc_final: 0.8449 (m) REVERT: F 336 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6384 (pt) REVERT: F 344 GLN cc_start: 0.7878 (mp10) cc_final: 0.7607 (mp10) REVERT: F 442 PHE cc_start: 0.8648 (m-80) cc_final: 0.8283 (m-10) REVERT: G 39 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7566 (tm-30) REVERT: G 74 ASN cc_start: 0.8682 (t0) cc_final: 0.8244 (t0) REVERT: G 239 THR cc_start: 0.9012 (p) cc_final: 0.8770 (t) REVERT: G 306 MET cc_start: 0.9087 (mtm) cc_final: 0.8807 (mtm) REVERT: G 362 ASP cc_start: 0.8072 (t0) cc_final: 0.7816 (t0) REVERT: G 496 MET cc_start: 0.9002 (tpp) cc_final: 0.8667 (tmm) REVERT: G 500 ILE cc_start: 0.9263 (mt) cc_final: 0.8926 (mt) REVERT: G 571 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.7315 (p90) REVERT: H 5 ASN cc_start: 0.8955 (t0) cc_final: 0.8714 (t0) REVERT: H 32 GLN cc_start: 0.8790 (pt0) cc_final: 0.8547 (pt0) REVERT: H 57 MET cc_start: 0.7375 (mtp) cc_final: 0.7055 (tmm) REVERT: H 59 GLU cc_start: 0.8366 (tt0) cc_final: 0.7995 (tt0) REVERT: H 61 MET cc_start: 0.6664 (tpt) cc_final: 0.6279 (tpt) REVERT: H 68 MET cc_start: 0.7372 (ptt) cc_final: 0.6902 (ptp) REVERT: H 152 SER cc_start: 0.9510 (m) cc_final: 0.9264 (m) REVERT: H 261 MET cc_start: 0.8416 (mmt) cc_final: 0.8004 (mmm) REVERT: H 265 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8781 (tt) REVERT: H 277 TYR cc_start: 0.8512 (m-10) cc_final: 0.8260 (m-80) REVERT: H 279 ARG cc_start: 0.8658 (mtm110) cc_final: 0.8186 (mtp-110) REVERT: H 284 GLN cc_start: 0.8488 (mt0) cc_final: 0.7717 (mt0) REVERT: I 60 ILE cc_start: 0.8943 (mt) cc_final: 0.8734 (tt) REVERT: I 70 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9142 (mp) REVERT: I 72 MET cc_start: 0.9074 (tpp) cc_final: 0.8784 (tpp) REVERT: I 76 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7954 (t80) REVERT: I 185 TYR cc_start: 0.9002 (m-80) cc_final: 0.8631 (m-80) REVERT: I 208 ASP cc_start: 0.8902 (t70) cc_final: 0.8606 (t70) REVERT: P 152 ILE cc_start: 0.9000 (mt) cc_final: 0.8764 (mp) REVERT: P 209 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.6825 (ptp-110) REVERT: P 210 GLU cc_start: 0.8105 (mp0) cc_final: 0.7881 (mp0) REVERT: P 298 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6749 (t80) REVERT: P 348 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8590 (mtpt) REVERT: Q 112 MET cc_start: 0.8700 (mmm) cc_final: 0.8478 (mmm) REVERT: Q 160 TYR cc_start: 0.7527 (t80) cc_final: 0.7268 (t80) REVERT: R 33 HIS cc_start: 0.1391 (OUTLIER) cc_final: 0.0693 (t-90) REVERT: R 75 ARG cc_start: 0.7647 (mmp80) cc_final: 0.7287 (mmp80) REVERT: R 76 ILE cc_start: 0.8967 (pt) cc_final: 0.8674 (mt) REVERT: R 94 ASN cc_start: 0.8001 (t0) cc_final: 0.7734 (t0) REVERT: R 103 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8298 (t) REVERT: S 64 LYS cc_start: 0.8570 (mtpp) cc_final: 0.7524 (mtmt) REVERT: T 82 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7824 (mmm-85) REVERT: T 111 ASP cc_start: 0.8764 (t0) cc_final: 0.8121 (p0) REVERT: T 117 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8747 (mm-30) REVERT: V 45 ARG cc_start: 0.8775 (ttt90) cc_final: 0.8481 (ttp80) REVERT: V 110 ASN cc_start: 0.7916 (t0) cc_final: 0.7249 (t0) REVERT: W 32 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8029 (mtpt) REVERT: W 68 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8138 (tm-30) REVERT: W 69 MET cc_start: 0.9154 (mmt) cc_final: 0.8792 (mmt) REVERT: W 78 ASP cc_start: 0.8337 (t0) cc_final: 0.7904 (t0) REVERT: W 84 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8821 (tt) REVERT: W 92 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7880 (mm-30) REVERT: W 127 MET cc_start: 0.8364 (ppp) cc_final: 0.7979 (ppp) REVERT: X 22 SER cc_start: 0.9264 (p) cc_final: 0.8818 (m) REVERT: X 26 LYS cc_start: 0.8645 (tttt) cc_final: 0.8404 (tttt) REVERT: X 102 GLN cc_start: 0.8378 (pm20) cc_final: 0.8133 (pm20) REVERT: Z 125 TYR cc_start: 0.8881 (m-80) cc_final: 0.8644 (m-80) REVERT: Z 142 TRP cc_start: 0.8678 (m-10) cc_final: 0.8279 (m-90) REVERT: a 46 TYR cc_start: 0.9143 (t80) cc_final: 0.8878 (t80) REVERT: a 51 ASP cc_start: 0.7530 (m-30) cc_final: 0.6767 (m-30) REVERT: a 54 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8438 (mm) REVERT: b 44 MET cc_start: 0.9105 (mpp) cc_final: 0.8687 (mpp) REVERT: q 49 TYR cc_start: 0.7500 (m-80) cc_final: 0.7003 (m-80) REVERT: q 68 MET cc_start: 0.4041 (OUTLIER) cc_final: 0.3333 (ttt) REVERT: q 81 MET cc_start: 0.6844 (mtt) cc_final: 0.6349 (mtt) outliers start: 138 outliers final: 81 residues processed: 933 average time/residue: 0.2035 time to fit residues: 311.6862 Evaluate side-chains 908 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 806 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER 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 D residue 94 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 348 LYS Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 126 PHE Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain W residue 32 LYS Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 68 MET Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 96 THR Chi-restraints excluded: chain s residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 75 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 378 optimal weight: 0.8980 chunk 393 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 341 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS H 169 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS H 304 HIS I 159 GLN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.118175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.090084 restraints weight = 75011.192| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.08 r_work: 0.3159 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 34756 Z= 0.199 Angle : 0.967 78.378 47115 Z= 0.361 Chirality : 0.046 0.243 5133 Planarity : 0.005 0.131 5959 Dihedral : 9.067 158.901 4934 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.72 % Favored : 96.26 % Rotamer: Outliers : 3.92 % Allowed : 21.72 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.31 (0.13), residues: 4118 helix: 0.81 (0.12), residues: 1883 sheet: -1.27 (0.25), residues: 399 loop : -0.97 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 266 TYR 0.036 0.002 TYR C 63 PHE 0.024 0.002 PHE a 3 TRP 0.028 0.002 TRP P 134 HIS 0.009 0.001 HIS T 103 Details of bonding type rmsd covalent geometry : bond 0.00474 (34715) covalent geometry : angle 0.72474 (47023) SS BOND : bond 0.00778 ( 4) SS BOND : angle 1.69669 ( 8) hydrogen bonds : bond 0.04148 ( 1407) hydrogen bonds : angle 4.91004 ( 4104) metal coordination : bond 0.02102 ( 37) metal coordination : angle 15.15447 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 834 time to evaluate : 1.379 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: A 4 TYR cc_start: 0.9050 (m-80) cc_final: 0.8702 (m-10) REVERT: A 10 ASN cc_start: 0.8328 (t160) cc_final: 0.7719 (t0) REVERT: B 72 GLU cc_start: 0.8886 (tp30) cc_final: 0.8424 (tt0) REVERT: B 95 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.5600 (m-80) REVERT: B 107 MET cc_start: 0.8834 (ttp) cc_final: 0.8633 (ttp) REVERT: B 115 ASP cc_start: 0.9301 (OUTLIER) cc_final: 0.8984 (t0) REVERT: B 220 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8874 (tp) REVERT: C 58 SER cc_start: 0.9242 (t) cc_final: 0.9020 (p) REVERT: C 149 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8496 (pp) REVERT: C 211 TYR cc_start: 0.9298 (t80) cc_final: 0.8934 (t80) REVERT: C 238 TRP cc_start: 0.8982 (m100) cc_final: 0.8717 (m100) REVERT: D 137 ASP cc_start: 0.8597 (m-30) cc_final: 0.7752 (m-30) REVERT: D 144 MET cc_start: 0.8194 (mpp) cc_final: 0.7988 (mpp) REVERT: D 148 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8172 (mt-10) REVERT: D 208 GLU cc_start: 0.8331 (tp30) cc_final: 0.8041 (tm-30) REVERT: D 212 GLU cc_start: 0.8313 (tp30) cc_final: 0.8058 (tp30) REVERT: D 215 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8499 (tm-30) REVERT: D 259 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8895 (tp30) REVERT: E 91 TRP cc_start: 0.7885 (t-100) cc_final: 0.7591 (t-100) REVERT: E 121 TYR cc_start: 0.8872 (m-80) cc_final: 0.8609 (m-80) REVERT: E 167 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8118 (tp) REVERT: E 184 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6819 (tmm) REVERT: E 245 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6153 (pp30) REVERT: F 53 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8307 (pp) REVERT: F 134 ASP cc_start: 0.7914 (t0) cc_final: 0.7149 (t0) REVERT: F 147 ARG cc_start: 0.7907 (ttt90) cc_final: 0.7544 (ttm-80) REVERT: F 149 MET cc_start: 0.7617 (mtp) cc_final: 0.7136 (mmp) REVERT: F 315 LEU cc_start: 0.8930 (mt) cc_final: 0.8474 (mt) REVERT: F 332 CYS cc_start: 0.8644 (m) cc_final: 0.8429 (m) REVERT: F 336 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6360 (mp) REVERT: F 442 PHE cc_start: 0.8679 (m-80) cc_final: 0.8329 (m-10) REVERT: G 39 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7667 (tm-30) REVERT: G 74 ASN cc_start: 0.8741 (t0) cc_final: 0.8306 (t0) REVERT: G 239 THR cc_start: 0.9112 (p) cc_final: 0.8909 (t) REVERT: G 295 ASP cc_start: 0.8280 (t70) cc_final: 0.8048 (t0) REVERT: G 306 MET cc_start: 0.9120 (mtm) cc_final: 0.8880 (mtm) REVERT: G 496 MET cc_start: 0.9010 (tpp) cc_final: 0.8647 (tmm) REVERT: G 500 ILE cc_start: 0.9277 (mt) cc_final: 0.8878 (mt) REVERT: G 530 TYR cc_start: 0.8763 (m-80) cc_final: 0.7951 (m-80) REVERT: G 571 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.7405 (p90) REVERT: G 579 MET cc_start: 0.8304 (ptm) cc_final: 0.7828 (tmm) REVERT: G 705 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8500 (mp10) REVERT: H 1 MET cc_start: 0.8617 (tpp) cc_final: 0.8384 (tpp) REVERT: H 5 ASN cc_start: 0.9093 (t0) cc_final: 0.8837 (t0) REVERT: H 57 MET cc_start: 0.7399 (mtp) cc_final: 0.6990 (tmm) REVERT: H 59 GLU cc_start: 0.8480 (tt0) cc_final: 0.8211 (tt0) REVERT: H 68 MET cc_start: 0.7431 (ptt) cc_final: 0.6908 (ptp) REVERT: H 152 SER cc_start: 0.9521 (m) cc_final: 0.8989 (t) REVERT: H 261 MET cc_start: 0.8415 (mmt) cc_final: 0.8020 (mmm) REVERT: H 265 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8853 (tt) REVERT: H 277 TYR cc_start: 0.8580 (m-10) cc_final: 0.8330 (m-80) REVERT: H 279 ARG cc_start: 0.8626 (mtm110) cc_final: 0.7913 (mtm110) REVERT: H 284 GLN cc_start: 0.8537 (mt0) cc_final: 0.7789 (mt0) REVERT: I 70 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9153 (mp) REVERT: I 72 MET cc_start: 0.9103 (tpp) cc_final: 0.8784 (tpp) REVERT: I 76 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7929 (t80) REVERT: I 208 ASP cc_start: 0.8900 (t70) cc_final: 0.8657 (t70) REVERT: P 152 ILE cc_start: 0.9014 (mt) cc_final: 0.8776 (mp) REVERT: P 210 GLU cc_start: 0.8229 (mp0) cc_final: 0.7973 (mp0) REVERT: P 219 ASN cc_start: 0.6502 (OUTLIER) cc_final: 0.6008 (t0) REVERT: P 298 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6834 (t80) REVERT: P 348 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8612 (mtpt) REVERT: R 33 HIS cc_start: 0.1430 (OUTLIER) cc_final: 0.0758 (t-90) REVERT: R 75 ARG cc_start: 0.7583 (mmp80) cc_final: 0.7234 (mmp80) REVERT: R 94 ASN cc_start: 0.7976 (t0) cc_final: 0.7632 (t0) REVERT: R 95 LEU cc_start: 0.6767 (mt) cc_final: 0.6523 (mt) REVERT: R 103 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8201 (t) REVERT: S 64 LYS cc_start: 0.8654 (mtpp) cc_final: 0.7676 (mtmt) REVERT: T 82 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8144 (tpp80) REVERT: T 117 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8865 (mt-10) REVERT: T 120 MET cc_start: 0.8473 (mtp) cc_final: 0.8234 (mtm) REVERT: T 125 GLU cc_start: 0.8545 (tp30) cc_final: 0.7952 (tp30) REVERT: T 126 PHE cc_start: 0.7658 (m-10) cc_final: 0.7086 (m-10) REVERT: V 45 ARG cc_start: 0.8790 (ttt90) cc_final: 0.8427 (ttp80) REVERT: V 110 ASN cc_start: 0.8066 (t0) cc_final: 0.7322 (t0) REVERT: W 32 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8126 (mmmt) REVERT: W 43 TYR cc_start: 0.9072 (t80) cc_final: 0.8605 (t80) REVERT: W 68 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8274 (tm-30) REVERT: W 69 MET cc_start: 0.9156 (mmt) cc_final: 0.8753 (mmt) REVERT: W 78 ASP cc_start: 0.8503 (t0) cc_final: 0.8070 (t0) REVERT: W 84 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8897 (tt) REVERT: W 92 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7991 (mm-30) REVERT: W 127 MET cc_start: 0.8501 (ppp) cc_final: 0.8095 (ppp) REVERT: X 22 SER cc_start: 0.9316 (p) cc_final: 0.8974 (p) REVERT: X 102 GLN cc_start: 0.8351 (pm20) cc_final: 0.8143 (pm20) REVERT: Z 98 MET cc_start: 0.6488 (ttm) cc_final: 0.5529 (mmt) REVERT: Z 142 TRP cc_start: 0.8672 (m-10) cc_final: 0.8293 (m-90) REVERT: a 46 TYR cc_start: 0.9132 (t80) cc_final: 0.8889 (t80) REVERT: a 51 ASP cc_start: 0.7632 (m-30) cc_final: 0.7193 (m-30) REVERT: b 44 MET cc_start: 0.9018 (mpp) cc_final: 0.8630 (mpp) REVERT: q 49 TYR cc_start: 0.7616 (m-80) cc_final: 0.7115 (m-80) REVERT: q 68 MET cc_start: 0.3917 (OUTLIER) cc_final: 0.3398 (ttt) REVERT: q 81 MET cc_start: 0.6887 (mtt) cc_final: 0.6451 (mtt) REVERT: q 93 MET cc_start: 0.7960 (mmm) cc_final: 0.7369 (mmm) REVERT: q 132 LYS cc_start: 0.8655 (ptmt) cc_final: 0.8000 (ptmt) outliers start: 142 outliers final: 90 residues processed: 913 average time/residue: 0.2054 time to fit residues: 307.9870 Evaluate side-chains 887 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 775 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER 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 D residue 123 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 705 GLN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 348 LYS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain W residue 32 LYS Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 68 MET Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 96 THR Chi-restraints excluded: chain r residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 335 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 285 optimal weight: 7.9990 chunk 297 optimal weight: 0.9980 chunk 290 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 399 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN D 349 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN F 455 GLN G 202 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 238 GLN Q 123 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 HIS X 77 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.092177 restraints weight = 73706.667| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.11 r_work: 0.3182 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 34756 Z= 0.143 Angle : 0.924 76.632 47115 Z= 0.346 Chirality : 0.044 0.233 5133 Planarity : 0.005 0.128 5959 Dihedral : 8.967 168.329 4934 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.74 % Favored : 96.24 % Rotamer: Outliers : 3.04 % Allowed : 23.00 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.28 (0.13), residues: 4118 helix: 0.85 (0.12), residues: 1881 sheet: -1.21 (0.25), residues: 401 loop : -0.98 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 267 TYR 0.036 0.002 TYR C 63 PHE 0.022 0.002 PHE a 3 TRP 0.033 0.001 TRP P 134 HIS 0.008 0.001 HIS G 444 Details of bonding type rmsd covalent geometry : bond 0.00338 (34715) covalent geometry : angle 0.70138 (47023) SS BOND : bond 0.00622 ( 4) SS BOND : angle 1.02372 ( 8) hydrogen bonds : bond 0.03933 ( 1407) hydrogen bonds : angle 4.81788 ( 4104) metal coordination : bond 0.01480 ( 37) metal coordination : angle 14.27218 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 842 time to evaluate : 1.155 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 10 ASN cc_start: 0.8225 (t160) cc_final: 0.7557 (t0) REVERT: A 105 GLU cc_start: 0.9176 (tp30) cc_final: 0.8723 (tm-30) REVERT: B 95 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.5266 (m-80) REVERT: B 107 MET cc_start: 0.8888 (ttp) cc_final: 0.8497 (ttm) REVERT: B 115 ASP cc_start: 0.9253 (m-30) cc_final: 0.8902 (t0) REVERT: B 220 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8747 (tp) REVERT: C 58 SER cc_start: 0.9268 (t) cc_final: 0.9004 (p) REVERT: C 149 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8463 (pp) REVERT: C 211 TYR cc_start: 0.9300 (t80) cc_final: 0.9019 (t80) REVERT: C 238 TRP cc_start: 0.8917 (m100) cc_final: 0.8667 (m100) REVERT: D 92 HIS cc_start: 0.6112 (m90) cc_final: 0.5363 (m90) REVERT: D 95 LEU cc_start: 0.9013 (mt) cc_final: 0.8522 (mt) REVERT: D 144 MET cc_start: 0.8195 (mpp) cc_final: 0.7991 (mpp) REVERT: D 202 TRP cc_start: 0.8994 (m-10) cc_final: 0.8775 (m-10) REVERT: D 208 GLU cc_start: 0.8345 (tp30) cc_final: 0.8031 (tm-30) REVERT: D 212 GLU cc_start: 0.8291 (tp30) cc_final: 0.8088 (tp30) REVERT: D 215 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8414 (tm-30) REVERT: E 91 TRP cc_start: 0.7827 (t-100) cc_final: 0.7485 (t-100) REVERT: E 167 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8129 (tp) REVERT: E 184 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6565 (tmm) REVERT: E 218 ARG cc_start: 0.6863 (mtp85) cc_final: 0.6654 (mtp85) REVERT: E 245 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6133 (pp30) REVERT: F 101 PHE cc_start: 0.8648 (m-80) cc_final: 0.8298 (m-80) REVERT: F 134 ASP cc_start: 0.7910 (t0) cc_final: 0.7164 (t0) REVERT: F 147 ARG cc_start: 0.7822 (ttt90) cc_final: 0.7449 (ttm-80) REVERT: F 311 TRP cc_start: 0.7644 (t60) cc_final: 0.7342 (t60) REVERT: F 315 LEU cc_start: 0.8909 (mt) cc_final: 0.8451 (mt) REVERT: F 332 CYS cc_start: 0.8653 (m) cc_final: 0.8401 (m) REVERT: F 336 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6194 (mp) REVERT: F 442 PHE cc_start: 0.8607 (m-80) cc_final: 0.8238 (m-10) REVERT: G 39 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7625 (tm-30) REVERT: G 74 ASN cc_start: 0.8645 (m-40) cc_final: 0.8209 (t0) REVERT: G 239 THR cc_start: 0.9057 (p) cc_final: 0.8819 (t) REVERT: G 295 ASP cc_start: 0.8174 (t70) cc_final: 0.7916 (t0) REVERT: G 306 MET cc_start: 0.9116 (mtm) cc_final: 0.8859 (mtm) REVERT: G 496 MET cc_start: 0.9008 (tpp) cc_final: 0.8689 (tmm) REVERT: G 500 ILE cc_start: 0.9261 (mt) cc_final: 0.8885 (mt) REVERT: G 571 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.7350 (p90) REVERT: G 579 MET cc_start: 0.8218 (ptm) cc_final: 0.7668 (tmm) REVERT: G 705 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: H 1 MET cc_start: 0.8628 (tpp) cc_final: 0.8336 (tpp) REVERT: H 59 GLU cc_start: 0.8330 (tt0) cc_final: 0.7988 (tt0) REVERT: H 68 MET cc_start: 0.7442 (ptt) cc_final: 0.6985 (ptp) REVERT: H 152 SER cc_start: 0.9326 (m) cc_final: 0.8995 (t) REVERT: H 173 TRP cc_start: 0.8322 (m-10) cc_final: 0.7826 (m-90) REVERT: H 261 MET cc_start: 0.8396 (mmt) cc_final: 0.8014 (mmm) REVERT: H 277 TYR cc_start: 0.8455 (m-10) cc_final: 0.8193 (m-80) REVERT: H 279 ARG cc_start: 0.8577 (mtm110) cc_final: 0.7834 (mtm110) REVERT: H 284 GLN cc_start: 0.8487 (mt0) cc_final: 0.7737 (mt0) REVERT: I 70 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9047 (mp) REVERT: I 72 MET cc_start: 0.9008 (tpp) cc_final: 0.8717 (tpp) REVERT: I 76 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8021 (t80) REVERT: I 110 GLU cc_start: 0.8410 (tp30) cc_final: 0.8169 (tp30) REVERT: I 144 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8337 (ptm160) REVERT: I 208 ASP cc_start: 0.8910 (t70) cc_final: 0.8659 (t70) REVERT: P 152 ILE cc_start: 0.9009 (mt) cc_final: 0.8786 (mp) REVERT: P 348 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8611 (mmmt) REVERT: P 370 LYS cc_start: 0.7864 (pttt) cc_final: 0.7287 (tttt) REVERT: Q 112 MET cc_start: 0.8722 (mmm) cc_final: 0.8471 (mmm) REVERT: R 33 HIS cc_start: 0.1393 (OUTLIER) cc_final: 0.0748 (t-90) REVERT: R 75 ARG cc_start: 0.7600 (mmp80) cc_final: 0.7345 (mmp80) REVERT: R 76 ILE cc_start: 0.8994 (pt) cc_final: 0.8697 (mt) REVERT: R 94 ASN cc_start: 0.8031 (t0) cc_final: 0.7716 (t0) REVERT: R 95 LEU cc_start: 0.6698 (mt) cc_final: 0.6419 (mt) REVERT: R 103 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8006 (t) REVERT: S 35 ASP cc_start: 0.8718 (m-30) cc_final: 0.7892 (t70) REVERT: S 64 LYS cc_start: 0.8648 (mtpp) cc_final: 0.7538 (mtmt) REVERT: T 82 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8276 (tpp80) REVERT: T 97 LYS cc_start: 0.8333 (tmtt) cc_final: 0.8124 (tmtt) REVERT: T 117 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8722 (mm-30) REVERT: T 120 MET cc_start: 0.8498 (mtp) cc_final: 0.8107 (mtp) REVERT: T 125 GLU cc_start: 0.8588 (tp30) cc_final: 0.8188 (tp30) REVERT: T 126 PHE cc_start: 0.7514 (m-10) cc_final: 0.7089 (m-10) REVERT: V 33 ASP cc_start: 0.8709 (t0) cc_final: 0.8468 (m-30) REVERT: V 45 ARG cc_start: 0.8808 (ttt90) cc_final: 0.8356 (ttp80) REVERT: V 110 ASN cc_start: 0.8029 (t0) cc_final: 0.7269 (t0) REVERT: W 68 GLU cc_start: 0.8597 (tm-30) cc_final: 0.7690 (tm-30) REVERT: W 69 MET cc_start: 0.9133 (mmt) cc_final: 0.8515 (mmp) REVERT: W 78 ASP cc_start: 0.8493 (t0) cc_final: 0.8267 (t0) REVERT: W 84 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8870 (tt) REVERT: W 92 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7917 (mm-30) REVERT: W 127 MET cc_start: 0.8488 (ppp) cc_final: 0.8085 (ppp) REVERT: X 14 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8417 (tttt) REVERT: X 22 SER cc_start: 0.9359 (p) cc_final: 0.9033 (p) REVERT: X 44 MET cc_start: 0.9160 (mmm) cc_final: 0.8784 (mmm) REVERT: Z 45 PHE cc_start: 0.8265 (t80) cc_final: 0.7878 (t80) REVERT: Z 98 MET cc_start: 0.6649 (ttm) cc_final: 0.5738 (mmt) REVERT: Z 142 TRP cc_start: 0.8621 (m-10) cc_final: 0.8252 (m-10) REVERT: a 46 TYR cc_start: 0.9102 (t80) cc_final: 0.8837 (t80) REVERT: a 51 ASP cc_start: 0.7610 (m-30) cc_final: 0.7010 (m-30) REVERT: b 44 MET cc_start: 0.8960 (mpp) cc_final: 0.8592 (mpp) REVERT: q 49 TYR cc_start: 0.7588 (m-80) cc_final: 0.7100 (m-80) REVERT: q 68 MET cc_start: 0.3715 (OUTLIER) cc_final: 0.3238 (ttt) REVERT: q 81 MET cc_start: 0.6855 (mtt) cc_final: 0.6414 (mtt) REVERT: q 93 MET cc_start: 0.7921 (mmm) cc_final: 0.7321 (mmm) REVERT: q 132 LYS cc_start: 0.8665 (ptmt) cc_final: 0.8440 (ptmt) outliers start: 110 outliers final: 74 residues processed: 902 average time/residue: 0.2084 time to fit residues: 310.2763 Evaluate side-chains 891 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 800 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 138 SER 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 D residue 123 LEU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 705 GLN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 348 LYS Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 68 MET Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 279 optimal weight: 10.0000 chunk 383 optimal weight: 1.9990 chunk 390 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 212 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 349 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 705 GLN H 169 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS I 192 ASN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.118739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.091308 restraints weight = 73707.650| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.04 r_work: 0.3177 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34756 Z= 0.157 Angle : 0.947 77.797 47115 Z= 0.357 Chirality : 0.044 0.209 5133 Planarity : 0.005 0.128 5959 Dihedral : 8.953 168.252 4934 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 2.96 % Allowed : 23.44 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.22 (0.13), residues: 4118 helix: 0.90 (0.12), residues: 1875 sheet: -1.20 (0.25), residues: 401 loop : -0.96 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 134 TYR 0.044 0.002 TYR B 170 PHE 0.039 0.002 PHE s 80 TRP 0.032 0.001 TRP P 134 HIS 0.008 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00373 (34715) covalent geometry : angle 0.72251 (47023) SS BOND : bond 0.00656 ( 4) SS BOND : angle 3.80892 ( 8) hydrogen bonds : bond 0.03972 ( 1407) hydrogen bonds : angle 4.81794 ( 4104) metal coordination : bond 0.01592 ( 37) metal coordination : angle 14.48069 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 833 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8186 (t160) cc_final: 0.7615 (t0) REVERT: A 68 GLU cc_start: 0.8823 (tt0) cc_final: 0.8576 (mt-10) REVERT: A 105 GLU cc_start: 0.9225 (tp30) cc_final: 0.8848 (tm-30) REVERT: B 107 MET cc_start: 0.8909 (ttp) cc_final: 0.8628 (ttm) REVERT: B 115 ASP cc_start: 0.9235 (m-30) cc_final: 0.8890 (t0) REVERT: B 220 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8735 (tp) REVERT: C 58 SER cc_start: 0.9280 (t) cc_final: 0.9021 (p) REVERT: C 149 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8477 (pp) REVERT: C 211 TYR cc_start: 0.9302 (t80) cc_final: 0.9009 (t80) REVERT: C 238 TRP cc_start: 0.8900 (m100) cc_final: 0.8698 (m100) REVERT: D 92 HIS cc_start: 0.6143 (m90) cc_final: 0.5462 (m90) REVERT: D 95 LEU cc_start: 0.9040 (mt) cc_final: 0.8500 (mt) REVERT: D 144 MET cc_start: 0.8072 (mpp) cc_final: 0.7836 (mpp) REVERT: D 202 TRP cc_start: 0.9050 (m-10) cc_final: 0.8827 (m-10) REVERT: D 208 GLU cc_start: 0.8375 (tp30) cc_final: 0.8052 (tm-30) REVERT: D 212 GLU cc_start: 0.8308 (tp30) cc_final: 0.7939 (tp30) REVERT: D 215 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8409 (tm-30) REVERT: D 259 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8802 (tp30) REVERT: D 270 ASN cc_start: 0.9438 (m-40) cc_final: 0.9189 (m-40) REVERT: E 91 TRP cc_start: 0.7849 (t-100) cc_final: 0.7508 (t-100) REVERT: E 167 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8103 (tp) REVERT: E 184 MET cc_start: 0.7006 (tmm) cc_final: 0.6592 (tmm) REVERT: E 245 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6119 (pp30) REVERT: F 101 PHE cc_start: 0.8651 (m-80) cc_final: 0.8299 (m-80) REVERT: F 134 ASP cc_start: 0.7880 (t0) cc_final: 0.7130 (t0) REVERT: F 147 ARG cc_start: 0.7750 (ttt90) cc_final: 0.7427 (ttm-80) REVERT: F 149 MET cc_start: 0.7430 (mtp) cc_final: 0.7181 (mmp) REVERT: F 274 LYS cc_start: 0.8198 (tptp) cc_final: 0.7200 (tptp) REVERT: F 315 LEU cc_start: 0.8905 (mt) cc_final: 0.8462 (mt) REVERT: F 332 CYS cc_start: 0.8654 (m) cc_final: 0.8405 (m) REVERT: F 336 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6234 (mp) REVERT: F 442 PHE cc_start: 0.8642 (m-80) cc_final: 0.8252 (m-10) REVERT: G 39 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7637 (tm-30) REVERT: G 74 ASN cc_start: 0.8647 (m-40) cc_final: 0.8223 (t0) REVERT: G 204 MET cc_start: 0.8376 (ttm) cc_final: 0.8118 (ttm) REVERT: G 239 THR cc_start: 0.9067 (p) cc_final: 0.8837 (t) REVERT: G 284 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7690 (tm-30) REVERT: G 295 ASP cc_start: 0.8191 (t70) cc_final: 0.7955 (t0) REVERT: G 306 MET cc_start: 0.9117 (mtm) cc_final: 0.8876 (mtm) REVERT: G 496 MET cc_start: 0.8998 (tpp) cc_final: 0.8593 (tmm) REVERT: G 500 ILE cc_start: 0.9262 (mt) cc_final: 0.8852 (mt) REVERT: G 530 TYR cc_start: 0.8724 (m-80) cc_final: 0.7895 (m-80) REVERT: G 571 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.7343 (p90) REVERT: G 579 MET cc_start: 0.8270 (ptm) cc_final: 0.7415 (tmm) REVERT: G 653 LEU cc_start: 0.8970 (mt) cc_final: 0.8683 (mt) REVERT: G 705 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: H 1 MET cc_start: 0.8686 (tpp) cc_final: 0.8411 (tpp) REVERT: H 59 GLU cc_start: 0.8378 (tt0) cc_final: 0.8052 (tt0) REVERT: H 68 MET cc_start: 0.7421 (ptt) cc_final: 0.6978 (ptp) REVERT: H 152 SER cc_start: 0.9438 (m) cc_final: 0.9017 (t) REVERT: H 173 TRP cc_start: 0.8334 (m-10) cc_final: 0.7819 (m-90) REVERT: H 181 MET cc_start: 0.8399 (mtm) cc_final: 0.8096 (mtm) REVERT: H 233 LEU cc_start: 0.8977 (tp) cc_final: 0.8623 (tp) REVERT: H 261 MET cc_start: 0.8276 (mmt) cc_final: 0.7917 (mmm) REVERT: H 277 TYR cc_start: 0.8466 (m-10) cc_final: 0.8188 (m-80) REVERT: H 279 ARG cc_start: 0.8599 (mtm110) cc_final: 0.7859 (mtm110) REVERT: H 284 GLN cc_start: 0.8479 (mt0) cc_final: 0.7764 (mt0) REVERT: I 70 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9120 (mp) REVERT: I 72 MET cc_start: 0.8984 (tpp) cc_final: 0.8705 (tpp) REVERT: I 76 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8010 (t80) REVERT: I 110 GLU cc_start: 0.8490 (tp30) cc_final: 0.8217 (tp30) REVERT: I 144 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8306 (ptm160) REVERT: I 208 ASP cc_start: 0.8918 (t70) cc_final: 0.8679 (t70) REVERT: P 152 ILE cc_start: 0.8994 (mt) cc_final: 0.8767 (mp) REVERT: P 210 GLU cc_start: 0.7939 (mp0) cc_final: 0.7643 (pm20) REVERT: P 219 ASN cc_start: 0.6445 (OUTLIER) cc_final: 0.5886 (t0) REVERT: P 328 MET cc_start: 0.8103 (pmm) cc_final: 0.7800 (mpp) REVERT: P 370 LYS cc_start: 0.7835 (pttt) cc_final: 0.7254 (tttt) REVERT: Q 112 MET cc_start: 0.8763 (mmm) cc_final: 0.8481 (mmm) REVERT: R 33 HIS cc_start: 0.1442 (OUTLIER) cc_final: 0.0761 (t-90) REVERT: R 75 ARG cc_start: 0.7644 (mmp80) cc_final: 0.7282 (mmp80) REVERT: R 94 ASN cc_start: 0.8009 (t0) cc_final: 0.7795 (t0) REVERT: R 95 LEU cc_start: 0.6562 (mt) cc_final: 0.6109 (mt) REVERT: R 103 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7788 (t) REVERT: S 64 LYS cc_start: 0.8662 (mtpp) cc_final: 0.7537 (mtmt) REVERT: T 82 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8368 (tpp80) REVERT: T 111 ASP cc_start: 0.8876 (m-30) cc_final: 0.8385 (p0) REVERT: T 117 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8759 (mm-30) REVERT: T 125 GLU cc_start: 0.8670 (tp30) cc_final: 0.8308 (tp30) REVERT: T 126 PHE cc_start: 0.7526 (m-10) cc_final: 0.7201 (m-10) REVERT: V 33 ASP cc_start: 0.8674 (t0) cc_final: 0.8460 (m-30) REVERT: V 45 ARG cc_start: 0.8802 (ttt90) cc_final: 0.8329 (ttp80) REVERT: V 110 ASN cc_start: 0.8096 (t0) cc_final: 0.7330 (t0) REVERT: W 32 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8123 (mmmt) REVERT: W 53 MET cc_start: 0.7651 (mtt) cc_final: 0.7151 (mtt) REVERT: W 68 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8152 (tm-30) REVERT: W 69 MET cc_start: 0.9164 (mmt) cc_final: 0.8703 (mmp) REVERT: W 73 ASN cc_start: 0.9223 (m-40) cc_final: 0.8397 (t0) REVERT: W 78 ASP cc_start: 0.8528 (t0) cc_final: 0.8278 (t0) REVERT: W 84 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8862 (tt) REVERT: W 92 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8000 (mm-30) REVERT: W 127 MET cc_start: 0.8513 (ppp) cc_final: 0.8104 (ppp) REVERT: X 14 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8451 (tttt) REVERT: X 22 SER cc_start: 0.9315 (p) cc_final: 0.8909 (p) REVERT: X 44 MET cc_start: 0.9171 (mmm) cc_final: 0.8753 (mmm) REVERT: Z 45 PHE cc_start: 0.8294 (t80) cc_final: 0.7882 (t80) REVERT: Z 98 MET cc_start: 0.7035 (ttm) cc_final: 0.6302 (mmt) REVERT: Z 133 MET cc_start: 0.8233 (tpt) cc_final: 0.7881 (tpp) REVERT: Z 142 TRP cc_start: 0.8606 (m-10) cc_final: 0.8220 (m-10) REVERT: a 46 TYR cc_start: 0.9104 (t80) cc_final: 0.8855 (t80) REVERT: a 51 ASP cc_start: 0.7607 (m-30) cc_final: 0.7017 (m-30) REVERT: b 44 MET cc_start: 0.9022 (mpp) cc_final: 0.8634 (mpp) REVERT: q 49 TYR cc_start: 0.7646 (m-80) cc_final: 0.7213 (m-80) REVERT: q 68 MET cc_start: 0.3859 (OUTLIER) cc_final: 0.3318 (ttt) REVERT: q 81 MET cc_start: 0.6948 (mtt) cc_final: 0.6515 (mtt) REVERT: q 93 MET cc_start: 0.7948 (mmm) cc_final: 0.7349 (mmm) REVERT: q 132 LYS cc_start: 0.8649 (ptmt) cc_final: 0.8192 (ptmt) outliers start: 107 outliers final: 73 residues processed: 892 average time/residue: 0.2014 time to fit residues: 295.3791 Evaluate side-chains 893 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 804 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER 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 D residue 261 MET Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 705 GLN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain W residue 32 LYS Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 68 MET Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 96 THR Chi-restraints excluded: chain r residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 223 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 260 optimal weight: 20.0000 chunk 302 optimal weight: 0.9990 chunk 239 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 333 optimal weight: 0.9990 chunk 408 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN F 270 ASN ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 HIS ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.091874 restraints weight = 74423.427| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.07 r_work: 0.3188 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34756 Z= 0.147 Angle : 0.936 77.631 47115 Z= 0.354 Chirality : 0.044 0.205 5133 Planarity : 0.005 0.126 5959 Dihedral : 8.903 168.044 4934 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 2.54 % Allowed : 23.85 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.24 (0.13), residues: 4118 helix: 0.87 (0.12), residues: 1886 sheet: -1.24 (0.25), residues: 403 loop : -0.95 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 134 TYR 0.040 0.002 TYR P 271 PHE 0.045 0.002 PHE s 80 TRP 0.040 0.001 TRP P 134 HIS 0.006 0.001 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00348 (34715) covalent geometry : angle 0.71840 (47023) SS BOND : bond 0.00860 ( 4) SS BOND : angle 3.45440 ( 8) hydrogen bonds : bond 0.03923 ( 1407) hydrogen bonds : angle 4.80483 ( 4104) metal coordination : bond 0.01442 ( 37) metal coordination : angle 14.18481 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 827 time to evaluate : 1.349 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 10 ASN cc_start: 0.8221 (t160) cc_final: 0.7619 (t0) REVERT: A 68 GLU cc_start: 0.8782 (tt0) cc_final: 0.8508 (mt-10) REVERT: A 105 GLU cc_start: 0.9215 (tp30) cc_final: 0.8896 (tm-30) REVERT: B 107 MET cc_start: 0.8929 (ttp) cc_final: 0.8646 (ttm) REVERT: B 115 ASP cc_start: 0.9256 (m-30) cc_final: 0.8913 (t0) REVERT: B 220 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8747 (tp) REVERT: C 58 SER cc_start: 0.9265 (t) cc_final: 0.8997 (p) REVERT: C 149 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8475 (pp) REVERT: C 211 TYR cc_start: 0.9298 (t80) cc_final: 0.8994 (t80) REVERT: D 92 HIS cc_start: 0.6140 (m90) cc_final: 0.5417 (m90) REVERT: D 95 LEU cc_start: 0.9039 (mt) cc_final: 0.8491 (mt) REVERT: D 202 TRP cc_start: 0.9005 (m-10) cc_final: 0.8767 (m-10) REVERT: D 208 GLU cc_start: 0.8395 (tp30) cc_final: 0.8065 (tm-30) REVERT: D 215 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8443 (tm-30) REVERT: E 91 TRP cc_start: 0.7824 (t-100) cc_final: 0.7482 (t-100) REVERT: E 167 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8126 (tp) REVERT: E 184 MET cc_start: 0.6845 (tmm) cc_final: 0.6482 (tmm) REVERT: E 242 PHE cc_start: 0.8002 (t80) cc_final: 0.7795 (t80) REVERT: E 245 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6101 (pp30) REVERT: F 101 PHE cc_start: 0.8628 (m-80) cc_final: 0.8264 (m-80) REVERT: F 134 ASP cc_start: 0.7879 (t0) cc_final: 0.7143 (t0) REVERT: F 147 ARG cc_start: 0.7837 (ttt90) cc_final: 0.7453 (ttm-80) REVERT: F 149 MET cc_start: 0.7482 (mtp) cc_final: 0.7210 (mmp) REVERT: F 311 TRP cc_start: 0.7626 (t60) cc_final: 0.7321 (t60) REVERT: F 315 LEU cc_start: 0.8900 (mt) cc_final: 0.8460 (mt) REVERT: F 332 CYS cc_start: 0.8634 (m) cc_final: 0.8388 (m) REVERT: F 336 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6197 (mp) REVERT: F 344 GLN cc_start: 0.8034 (mp10) cc_final: 0.7746 (mp10) REVERT: F 442 PHE cc_start: 0.8581 (m-80) cc_final: 0.8193 (m-10) REVERT: G 39 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7628 (tm-30) REVERT: G 74 ASN cc_start: 0.8675 (m-40) cc_final: 0.8246 (t0) REVERT: G 239 THR cc_start: 0.9053 (p) cc_final: 0.8820 (t) REVERT: G 306 MET cc_start: 0.9110 (mtm) cc_final: 0.8876 (mtm) REVERT: G 496 MET cc_start: 0.8962 (tpp) cc_final: 0.8528 (tmm) REVERT: G 500 ILE cc_start: 0.9263 (mt) cc_final: 0.8789 (mt) REVERT: G 530 TYR cc_start: 0.8739 (m-80) cc_final: 0.7890 (m-80) REVERT: G 571 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.7359 (p90) REVERT: H 1 MET cc_start: 0.8652 (tpp) cc_final: 0.8364 (tpp) REVERT: H 59 GLU cc_start: 0.8239 (tt0) cc_final: 0.7900 (tt0) REVERT: H 68 MET cc_start: 0.7442 (ptt) cc_final: 0.7011 (ptp) REVERT: H 152 SER cc_start: 0.9493 (m) cc_final: 0.9069 (t) REVERT: H 173 TRP cc_start: 0.8308 (m-10) cc_final: 0.7156 (m-90) REVERT: H 181 MET cc_start: 0.8484 (mtm) cc_final: 0.8227 (mtm) REVERT: H 277 TYR cc_start: 0.8408 (m-10) cc_final: 0.8157 (m-80) REVERT: H 279 ARG cc_start: 0.8559 (mtm110) cc_final: 0.8132 (mtm-85) REVERT: I 70 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9038 (mp) REVERT: I 72 MET cc_start: 0.8974 (tpp) cc_final: 0.8716 (tpp) REVERT: I 76 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7995 (t80) REVERT: I 110 GLU cc_start: 0.8481 (tp30) cc_final: 0.8089 (tp30) REVERT: I 144 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8279 (ptm160) REVERT: I 208 ASP cc_start: 0.8904 (t70) cc_final: 0.8689 (t70) REVERT: P 152 ILE cc_start: 0.8986 (mt) cc_final: 0.8745 (mp) REVERT: P 210 GLU cc_start: 0.8011 (mp0) cc_final: 0.7809 (pm20) REVERT: P 215 ASN cc_start: 0.8456 (m110) cc_final: 0.8171 (m110) REVERT: P 219 ASN cc_start: 0.6518 (OUTLIER) cc_final: 0.5823 (t0) REVERT: P 328 MET cc_start: 0.8157 (pmm) cc_final: 0.7769 (mpp) REVERT: P 370 LYS cc_start: 0.7922 (pttt) cc_final: 0.7274 (tttt) REVERT: Q 69 GLU cc_start: 0.8604 (tp30) cc_final: 0.8179 (tp30) REVERT: Q 104 ARG cc_start: 0.8773 (mmt90) cc_final: 0.8542 (mmt90) REVERT: Q 112 MET cc_start: 0.8782 (mmm) cc_final: 0.8510 (mmm) REVERT: R 33 HIS cc_start: 0.1435 (OUTLIER) cc_final: 0.0762 (t-90) REVERT: R 75 ARG cc_start: 0.7655 (mmp80) cc_final: 0.7294 (mmp80) REVERT: R 103 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7780 (t) REVERT: S 64 LYS cc_start: 0.8654 (mtpp) cc_final: 0.7522 (mtmt) REVERT: T 82 ARG cc_start: 0.8788 (mmm-85) cc_final: 0.8455 (tpp80) REVERT: T 111 ASP cc_start: 0.8862 (m-30) cc_final: 0.8386 (p0) REVERT: T 117 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8792 (mm-30) REVERT: V 45 ARG cc_start: 0.8811 (ttt90) cc_final: 0.8319 (ttp80) REVERT: V 57 ASP cc_start: 0.9313 (m-30) cc_final: 0.8977 (m-30) REVERT: V 83 GLN cc_start: 0.8421 (tp40) cc_final: 0.8220 (tm-30) REVERT: V 110 ASN cc_start: 0.8069 (t0) cc_final: 0.7331 (t0) REVERT: W 32 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8062 (mmmt) REVERT: W 53 MET cc_start: 0.7555 (mtt) cc_final: 0.7091 (mtt) REVERT: W 68 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8179 (tm-30) REVERT: W 69 MET cc_start: 0.9178 (mmt) cc_final: 0.8717 (mmp) REVERT: W 73 ASN cc_start: 0.9182 (m-40) cc_final: 0.8326 (t0) REVERT: W 78 ASP cc_start: 0.8548 (t0) cc_final: 0.8297 (t0) REVERT: W 84 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8841 (tt) REVERT: W 92 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8014 (mm-30) REVERT: W 127 MET cc_start: 0.8490 (ppp) cc_final: 0.8078 (ppp) REVERT: X 14 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8453 (tttt) REVERT: X 22 SER cc_start: 0.9336 (p) cc_final: 0.8930 (p) REVERT: X 26 LYS cc_start: 0.8617 (tttt) cc_final: 0.8385 (tttt) REVERT: X 44 MET cc_start: 0.9190 (mmm) cc_final: 0.8778 (mmm) REVERT: X 102 GLN cc_start: 0.8033 (pm20) cc_final: 0.7549 (pm20) REVERT: Z 45 PHE cc_start: 0.8272 (t80) cc_final: 0.7897 (t80) REVERT: Z 98 MET cc_start: 0.7065 (ttm) cc_final: 0.6384 (mmt) REVERT: Z 133 MET cc_start: 0.8184 (tpt) cc_final: 0.7868 (tpp) REVERT: Z 142 TRP cc_start: 0.8584 (m-10) cc_final: 0.8231 (m-90) REVERT: a 46 TYR cc_start: 0.9089 (t80) cc_final: 0.8816 (t80) REVERT: a 51 ASP cc_start: 0.7617 (m-30) cc_final: 0.7290 (m-30) REVERT: b 15 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7948 (ptpt) REVERT: b 44 MET cc_start: 0.9030 (mpp) cc_final: 0.8619 (mpp) REVERT: q 49 TYR cc_start: 0.7681 (m-80) cc_final: 0.7219 (m-80) REVERT: q 60 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7884 (mtp85) REVERT: q 93 MET cc_start: 0.7938 (mmm) cc_final: 0.7338 (mmm) REVERT: q 132 LYS cc_start: 0.8578 (ptmt) cc_final: 0.8313 (ptmt) outliers start: 92 outliers final: 70 residues processed: 880 average time/residue: 0.2132 time to fit residues: 306.9859 Evaluate side-chains 885 residues out of total 3618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 801 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER 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 D residue 258 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 303 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain W residue 32 LYS Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain r residue 96 THR Chi-restraints excluded: chain r residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 394 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 316 optimal weight: 0.0050 chunk 307 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 397 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.091946 restraints weight = 73531.200| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.03 r_work: 0.3190 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 34756 Z= 0.229 Angle : 1.041 77.638 47115 Z= 0.459 Chirality : 0.047 0.927 5133 Planarity : 0.005 0.132 5959 Dihedral : 8.923 168.014 4934 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 2.87 % Allowed : 23.58 % Favored : 73.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.25 (0.13), residues: 4118 helix: 0.87 (0.12), residues: 1887 sheet: -1.24 (0.25), residues: 403 loop : -0.96 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG F 224 TYR 0.049 0.002 TYR D 214 PHE 0.037 0.002 PHE s 80 TRP 0.035 0.002 TRP P 134 HIS 0.006 0.001 HIS W 51 Details of bonding type rmsd covalent geometry : bond 0.00515 (34715) covalent geometry : angle 0.85159 (47023) SS BOND : bond 0.00600 ( 4) SS BOND : angle 3.17227 ( 8) hydrogen bonds : bond 0.03936 ( 1407) hydrogen bonds : angle 4.80722 ( 4104) metal coordination : bond 0.01444 ( 37) metal coordination : angle 14.18120 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9814.49 seconds wall clock time: 168 minutes 46.38 seconds (10126.38 seconds total)