Starting phenix.real_space_refine on Tue May 5 22:23:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnq_38511/05_2026/8xnq_38511_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnq_38511/05_2026/8xnq_38511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xnq_38511/05_2026/8xnq_38511_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnq_38511/05_2026/8xnq_38511_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xnq_38511/05_2026/8xnq_38511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnq_38511/05_2026/8xnq_38511.map" } resolution = 3.7 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= 0.071 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 21725 2.51 5 N 5756 2.21 5 O 6152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s 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: 33919 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 754 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3088 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 21, 'TRANS': 363} Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3288 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2510 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 22, 'TRANS': 291} 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: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 539 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'PC1': 1, 'SF4': 1, 'UQ1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 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 82.512 58.903 105.345 1.00 29.52 S ATOM 1520 SG CYS B 164 79.743 55.367 110.300 1.00 28.96 S ATOM 1750 SG CYS B 194 84.877 55.113 109.445 1.00 29.28 S ATOM 1023 SG CYS B 100 81.095 54.995 104.458 1.00 30.11 S ATOM 7530 SG CYS E 134 142.816 47.518 150.545 1.00 56.01 S ATOM 7564 SG CYS E 139 145.326 49.099 149.804 1.00 56.50 S ATOM 7848 SG CYS E 175 140.575 50.981 153.313 1.00 54.42 S ATOM 7871 SG CYS E 179 143.918 52.567 153.402 1.00 57.95 S ATOM 11401 SG CYS F 425 124.465 57.138 153.902 1.00 45.60 S ATOM 11079 SG CYS F 385 124.329 54.801 148.053 1.00 39.95 S ATOM 11059 SG CYS F 382 120.137 56.019 150.430 1.00 40.29 S ATOM 11040 SG CYS F 379 122.043 51.836 153.158 1.00 43.09 S ATOM 12449 SG CYS G 131 103.402 45.630 136.947 1.00 31.31 S ATOM 12428 SG CYS G 128 105.432 49.531 132.411 1.00 30.26 S ATOM 12489 SG CYS G 137 103.255 51.502 138.525 1.00 33.13 S ATOM 13174 SG CYS G 226 105.089 45.374 145.501 1.00 34.31 S ATOM 12845 SG CYS G 182 108.292 43.468 151.151 1.00 36.31 S ATOM 12821 SG CYS G 179 107.776 49.126 148.763 1.00 35.62 S ATOM 12798 SG CYS G 176 111.059 44.835 146.122 1.00 34.05 S ATOM 11935 SG CYS G 64 109.387 55.072 150.903 1.00 35.53 S ATOM 12021 SG CYS G 75 110.138 57.138 149.277 1.00 36.47 S ATOM 12046 SG CYS G 78 109.188 61.561 151.520 1.00 36.76 S ATOM 12147 SG CYS G 92 108.975 59.578 154.658 1.00 39.04 S ATOM 20147 SG CYS I 123 88.820 49.606 118.330 1.00 27.30 S ATOM 20373 SG CYS I 152 88.475 48.581 113.193 1.00 27.39 S ATOM 20420 SG CYS I 158 94.165 48.542 115.221 1.00 26.60 S ATOM 20399 SG CYS I 155 91.169 53.046 115.060 1.00 27.04 S ATOM 20096 SG CYS I 116 98.657 45.117 125.464 1.00 29.24 S ATOM 20119 SG CYS I 119 94.239 44.991 122.164 1.00 28.85 S ATOM 20077 SG CYS I 113 97.335 40.099 122.082 1.00 28.61 S ATOM 20449 SG CYS I 162 100.316 44.680 120.059 1.00 28.07 S ATOM 24958 SG CYS R 79 113.706 37.505 124.315 1.00 32.60 S ATOM 25134 SG CYS R 104 111.235 36.103 125.759 1.00 32.49 S ATOM 25156 SG CYS R 107 110.533 36.858 122.362 1.00 30.78 S Time building chain proxies: 6.84, per 1000 atoms: 0.20 Number of scatterers: 33919 At special positions: 0 Unit cell: (171.6, 127.6, 201.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 244 16.00 P 13 15.00 O 6152 8.00 N 5756 7.00 C 21725 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=2.09 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: 2.86 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 303 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 303 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 304 " pdb="FE3 SF4 I 304 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 304 " - pdb=" SG CYS I 162 " pdb="FE1 SF4 I 304 " - pdb=" SG CYS I 116 " pdb="FE2 SF4 I 304 " - pdb=" SG CYS I 119 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7810 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 35 sheets defined 49.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 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 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.585A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 3.644A 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: 3.590A 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: 4.114A 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: 3.855A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.297A 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: 3.849A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 159 removed outlier: 3.642A 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: 3.708A 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: 3.692A 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: 3.744A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.669A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.530A 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: 4.470A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.620A 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: 3.685A 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: 3.557A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.294A 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: 3.853A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.923A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.516A 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: 3.635A pdb=" N GLY F 188 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.832A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 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: 8.643A 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: 3.660A 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: 3.510A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.348A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.520A 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: 3.712A 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: 3.931A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.820A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.671A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.026A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.007A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.636A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.522A 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: 3.750A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.575A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 85 removed outlier: 3.741A pdb=" N THR H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 124 removed outlier: 3.686A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.853A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.735A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.538A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.529A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.864A 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: 3.804A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.874A 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: 4.026A 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: 4.106A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.597A 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: 3.661A pdb=" N ARG P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.610A 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: 4.412A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 4.200A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.185A 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: 3.625A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.676A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.856A 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: 3.518A 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: 3.527A 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 removed outlier: 3.669A pdb=" N TRP a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) 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: 3.758A 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: 3.601A 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: 4.125A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 17 Processing helix chain 's' and resid 78 through 88 removed outlier: 3.656A 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: 7.067A 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: 6.920A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) 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: 3.832A 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: 5.982A 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: 3.873A 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: 3.564A 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 82 removed outlier: 4.314A pdb=" N MET D 80 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG D 96 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 5.089A 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: 6.355A 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: 3.501A 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: 6.230A 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: 6.315A 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: 6.454A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.787A 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: 6.203A 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: 7.089A 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: 6.358A 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 '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: 3.646A 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) 1411 hydrogen bonds defined for protein. 4116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.80 Time building geometry restraints manager: 3.60 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: 11454 1.37 - 1.59: 22795 1.59 - 1.80: 266 1.80 - 2.02: 131 2.02 - 2.23: 80 Bond restraints: 34726 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.648 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 8.64e+01 ... (remaining 34721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.66: 46262 6.66 - 13.33: 610 13.33 - 19.99: 164 19.99 - 26.66: 1 26.66 - 33.32: 2 Bond angle restraints: 47039 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 89.11 25.53 1.52e+00 4.33e-01 2.82e+02 angle pdb=" N ILE G 251 " pdb=" CA ILE G 251 " pdb=" C ILE G 251 " ideal model delta sigma weight residual 108.17 126.84 -18.67 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 97.31 16.07 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 112.83 100.09 12.74 9.90e-01 1.02e+00 1.66e+02 angle pdb=" S1 FES G 803 " pdb="FE2 FES G 803 " pdb=" S2 FES G 803 " ideal model delta sigma weight residual 104.33 89.68 14.65 1.14e+00 7.69e-01 1.65e+02 ... (remaining 47034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.43: 20207 27.43 - 54.87: 667 54.87 - 82.30: 94 82.30 - 109.74: 9 109.74 - 137.17: 3 Dihedral angle restraints: 20980 sinusoidal: 8866 harmonic: 12114 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 -101.14 -21.46 0 2.50e+00 1.60e-01 7.37e+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 31.37 61.63 1 1.00e+01 1.00e-02 5.04e+01 ... (remaining 20977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4507 0.183 - 0.366: 550 0.366 - 0.549: 49 0.549 - 0.732: 4 0.732 - 0.915: 24 Chirality restraints: 5134 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 -0.91 2.00e-01 2.50e+01 2.09e+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 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 9.65 0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 5131 not shown) Planarity restraints: 5962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 401 " -0.016 2.00e-02 2.50e+03 2.20e-01 1.46e+03 pdb=" C1M UQ9 H 401 " -0.109 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 401 " 0.027 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 401 " -0.051 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 401 " 0.089 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 401 " -0.122 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 401 " 0.036 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " 0.271 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 401 " 0.134 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 401 " -0.256 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 401 " 0.437 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 401 " -0.441 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 H 401 " 0.191 2.00e-02 2.50e+03 2.58e-01 8.29e+02 pdb=" C11 UQ9 H 401 " 0.037 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " 0.304 2.00e-02 2.50e+03 pdb=" C8 UQ9 H 401 " -0.439 2.00e-02 2.50e+03 pdb=" C9 UQ9 H 401 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 UQ9 H 401 " 0.222 2.00e-02 2.50e+03 1.87e-01 4.38e+02 pdb=" C23 UQ9 H 401 " -0.309 2.00e-02 2.50e+03 pdb=" C24 UQ9 H 401 " -0.070 2.00e-02 2.50e+03 pdb=" C25 UQ9 H 401 " -0.003 2.00e-02 2.50e+03 pdb=" C26 UQ9 H 401 " 0.160 2.00e-02 2.50e+03 ... (remaining 5959 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 82 2.38 - 3.01: 22639 3.01 - 3.64: 53104 3.64 - 4.27: 83168 4.27 - 4.90: 135020 Nonbonded interactions: 294013 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 1.903 3.040 nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.941 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.970 3.040 nonbonded pdb=" OD1 ASN P 376 " pdb=" N TYR P 377 " model vdw 1.980 3.120 ... (remaining 294008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 36.470 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 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 34767 Z= 1.051 Angle : 2.280 52.571 47131 Z= 1.523 Chirality : 0.133 0.915 5134 Planarity : 0.009 0.258 5962 Dihedral : 13.515 137.171 13158 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 46.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % Rotamer: Outliers : 0.33 % Allowed : 7.85 % Favored : 91.82 % Cbeta Deviations : 1.87 % 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: -2.08 (0.12), residues: 4121 helix: -0.74 (0.11), residues: 1804 sheet: -1.17 (0.27), residues: 360 loop : -2.02 (0.13), residues: 1957 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 0.029 0.002 PHE D 200 TRP 0.034 0.002 TRP G 285 HIS 0.018 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.01469 (34726) covalent geometry : angle 2.15442 (47039) SS BOND : bond 0.03600 ( 4) SS BOND : angle 5.78390 ( 8) hydrogen bonds : bond 0.24403 ( 1411) hydrogen bonds : angle 8.85727 ( 4116) metal coordination : bond 0.52816 ( 37) metal coordination : angle 17.72237 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1668 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1656 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 89 ILE cc_start: 0.8709 (mm) cc_final: 0.8481 (mm) REVERT: B 174 SER cc_start: 0.8287 (t) cc_final: 0.7860 (t) REVERT: B 176 SER cc_start: 0.8701 (m) cc_final: 0.7962 (m) REVERT: C 129 TYR cc_start: 0.7993 (m-80) cc_final: 0.7643 (m-80) REVERT: C 134 LEU cc_start: 0.8074 (mp) cc_final: 0.7601 (mt) REVERT: D 144 MET cc_start: 0.8071 (mpp) cc_final: 0.7513 (mpp) REVERT: D 277 VAL cc_start: 0.8130 (t) cc_final: 0.7829 (p) REVERT: D 375 MET cc_start: 0.7704 (tpp) cc_final: 0.7504 (tpp) REVERT: F 124 THR cc_start: 0.7474 (m) cc_final: 0.7267 (m) REVERT: F 429 ASP cc_start: 0.6881 (m-30) cc_final: 0.6437 (m-30) REVERT: G 47 THR cc_start: 0.7895 (p) cc_final: 0.7467 (p) REVERT: G 427 LEU cc_start: 0.7841 (mt) cc_final: 0.7622 (mt) REVERT: G 620 TRP cc_start: 0.7459 (p-90) cc_final: 0.7247 (p-90) REVERT: H 43 TYR cc_start: 0.7695 (m-80) cc_final: 0.7142 (m-10) REVERT: H 99 ASN cc_start: 0.7979 (m-40) cc_final: 0.7625 (m110) REVERT: H 222 LEU cc_start: 0.8119 (mp) cc_final: 0.7770 (mp) REVERT: H 247 TYR cc_start: 0.6862 (t80) cc_final: 0.6635 (t80) REVERT: H 249 ILE cc_start: 0.8451 (pt) cc_final: 0.6495 (pt) REVERT: H 282 TYR cc_start: 0.6548 (t80) cc_final: 0.6141 (t80) REVERT: I 66 LEU cc_start: 0.8706 (mt) cc_final: 0.8422 (mt) REVERT: I 128 ILE cc_start: 0.8445 (mt) cc_final: 0.8164 (mt) REVERT: I 204 ASN cc_start: 0.7669 (m-40) cc_final: 0.7223 (m-40) REVERT: P 301 ILE cc_start: 0.7627 (mm) cc_final: 0.7383 (mm) REVERT: Q 96 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8686 (mttp) REVERT: Q 101 PHE cc_start: 0.8572 (m-80) cc_final: 0.8363 (m-80) REVERT: V 83 GLN cc_start: 0.7955 (tp40) cc_final: 0.7698 (tm-30) REVERT: X 18 VAL cc_start: 0.6647 (t) cc_final: 0.6445 (t) REVERT: Z 65 LEU cc_start: 0.7705 (mt) cc_final: 0.7037 (mt) REVERT: a 47 LEU cc_start: 0.8587 (mp) cc_final: 0.7849 (mp) REVERT: b 51 TYR cc_start: 0.7346 (m-80) cc_final: 0.7039 (t80) REVERT: q 26 VAL cc_start: 0.6860 (t) cc_final: 0.6524 (t) REVERT: r 101 MET cc_start: 0.7504 (ttp) cc_final: 0.7193 (ttm) outliers start: 12 outliers final: 0 residues processed: 1665 average time/residue: 0.2250 time to fit residues: 586.6500 Evaluate side-chains 999 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 998 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 96 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.0270 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 151 GLN B 209 GLN C 88 HIS C 123 ASN C 130 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS D 87 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN D 346 GLN D 381 HIS ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 88 GLN E 152 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 HIS ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN G 123 ASN G 140 GLN G 164 ASN G 202 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 495 ASN G 498 GLN ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN H 124 ASN H 169 GLN H 171 HIS H 292 ASN I 126 GLN I 204 ASN P 71 ASN ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 HIS P 215 ASN ** P 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 ASN P 341 GLN Q 51 GLN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 HIS V 21 HIS W 73 ASN X 30 HIS ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN a 58 ASN b 52 ASN b 71 GLN q 13 GLN q 31 ASN q 54 GLN r 21 GLN r 110 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.110151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087501 restraints weight = 102288.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090742 restraints weight = 48545.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.092969 restraints weight = 26719.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092737 restraints weight = 20793.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.092877 restraints weight = 19761.284| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 34767 Z= 0.205 Angle : 1.056 70.577 47131 Z= 0.452 Chirality : 0.050 0.211 5134 Planarity : 0.007 0.120 5962 Dihedral : 9.941 150.422 4940 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.04 % Rotamer: Outliers : 4.01 % Allowed : 18.15 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4121 helix: 0.15 (0.11), residues: 1889 sheet: -0.97 (0.27), residues: 360 loop : -1.38 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 26 TYR 0.027 0.003 TYR B 112 PHE 0.026 0.003 PHE H 310 TRP 0.046 0.002 TRP D 300 HIS 0.012 0.002 HIS P 285 Details of bonding type rmsd covalent geometry : bond 0.00459 (34726) covalent geometry : angle 0.87607 (47039) SS BOND : bond 0.00463 ( 4) SS BOND : angle 1.61707 ( 8) hydrogen bonds : bond 0.05953 ( 1411) hydrogen bonds : angle 5.73904 ( 4116) metal coordination : bond 0.02398 ( 37) metal coordination : angle 13.97584 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1128 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5366 (tpp) REVERT: A 18 ILE cc_start: 0.9263 (mm) cc_final: 0.8981 (mm) REVERT: A 24 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8875 (tp) REVERT: A 54 LYS cc_start: 0.8364 (ptmt) cc_final: 0.8102 (ptmt) REVERT: A 104 TYR cc_start: 0.8578 (t80) cc_final: 0.8306 (t80) REVERT: B 88 SER cc_start: 0.9318 (p) cc_final: 0.9111 (t) REVERT: B 112 TYR cc_start: 0.7242 (m-80) cc_final: 0.7000 (m-80) REVERT: B 122 ARG cc_start: 0.8943 (pmt170) cc_final: 0.8441 (pmt-80) REVERT: B 147 LYS cc_start: 0.8959 (mttt) cc_final: 0.8611 (ttpt) REVERT: B 157 TYR cc_start: 0.8328 (m-80) cc_final: 0.8075 (m-80) REVERT: B 215 GLU cc_start: 0.7716 (tp30) cc_final: 0.7498 (tp30) REVERT: C 93 ILE cc_start: 0.8853 (mm) cc_final: 0.8541 (mt) REVERT: C 153 ASP cc_start: 0.8367 (t0) cc_final: 0.8163 (t0) REVERT: C 172 MET cc_start: 0.8572 (mmm) cc_final: 0.8344 (mmm) REVERT: C 221 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7683 (mt-10) REVERT: D 156 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 185 MET cc_start: 0.8903 (tpp) cc_final: 0.8467 (tpt) REVERT: D 292 MET cc_start: 0.8504 (tpp) cc_final: 0.8215 (mmt) REVERT: D 443 MET cc_start: 0.8656 (mpp) cc_final: 0.8445 (mpp) REVERT: E 58 ASN cc_start: 0.8700 (m-40) cc_final: 0.8265 (m-40) REVERT: E 98 ASN cc_start: 0.8827 (m-40) cc_final: 0.7975 (m110) REVERT: E 105 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8126 (pm20) REVERT: E 113 GLU cc_start: 0.7677 (mt-10) cc_final: 0.6955 (mt-10) REVERT: E 118 TYR cc_start: 0.8425 (m-80) cc_final: 0.8001 (m-80) REVERT: E 184 MET cc_start: 0.7812 (ttm) cc_final: 0.7545 (ptp) REVERT: E 194 ASP cc_start: 0.7047 (t0) cc_final: 0.6325 (p0) REVERT: E 205 ASP cc_start: 0.8027 (m-30) cc_final: 0.7825 (m-30) REVERT: F 77 LEU cc_start: 0.9074 (tt) cc_final: 0.8812 (pp) REVERT: F 124 THR cc_start: 0.8292 (m) cc_final: 0.7965 (p) REVERT: F 155 TYR cc_start: 0.8489 (m-80) cc_final: 0.7959 (m-80) REVERT: F 168 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8143 (t0) REVERT: F 390 ASP cc_start: 0.7448 (t0) cc_final: 0.6637 (t70) REVERT: F 413 TRP cc_start: 0.8162 (t60) cc_final: 0.7829 (t60) REVERT: G 77 MET cc_start: 0.8334 (tpp) cc_final: 0.8107 (tpp) REVERT: G 100 TRP cc_start: 0.6324 (m100) cc_final: 0.6121 (m100) REVERT: G 138 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7712 (t0) REVERT: G 264 SER cc_start: 0.9301 (m) cc_final: 0.8676 (p) REVERT: G 283 GLU cc_start: 0.7918 (pm20) cc_final: 0.7528 (pt0) REVERT: G 347 ASP cc_start: 0.8412 (p0) cc_final: 0.7708 (p0) REVERT: G 427 LEU cc_start: 0.8887 (mt) cc_final: 0.8641 (mt) REVERT: G 670 GLU cc_start: 0.9334 (mm-30) cc_final: 0.9127 (mm-30) REVERT: G 707 MET cc_start: 0.9275 (mmm) cc_final: 0.9031 (mmm) REVERT: H 43 TYR cc_start: 0.8687 (m-80) cc_final: 0.8035 (m-10) REVERT: H 134 ARG cc_start: 0.8609 (ptm160) cc_final: 0.8313 (ptm160) REVERT: H 172 MET cc_start: 0.7380 (ppp) cc_final: 0.6939 (ppp) REVERT: H 181 MET cc_start: 0.8595 (mtt) cc_final: 0.7936 (mtt) REVERT: H 224 PHE cc_start: 0.8448 (t80) cc_final: 0.7921 (t80) REVERT: H 268 SER cc_start: 0.9398 (m) cc_final: 0.9030 (t) REVERT: H 282 TYR cc_start: 0.7729 (t80) cc_final: 0.7058 (t80) REVERT: H 286 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8054 (mpp) REVERT: I 42 LYS cc_start: 0.7124 (mmtt) cc_final: 0.6373 (tptt) REVERT: I 55 ASP cc_start: 0.8310 (m-30) cc_final: 0.8037 (t70) REVERT: I 63 TRP cc_start: 0.8687 (m-10) cc_final: 0.8380 (m-90) REVERT: I 208 ASP cc_start: 0.8076 (t0) cc_final: 0.7760 (t70) REVERT: P 169 HIS cc_start: 0.6941 (t-90) cc_final: 0.6656 (t-170) REVERT: P 174 MET cc_start: 0.6954 (tpp) cc_final: 0.6503 (tmm) REVERT: P 181 LEU cc_start: 0.8194 (mp) cc_final: 0.7789 (mm) REVERT: P 271 TYR cc_start: 0.7228 (m-80) cc_final: 0.6367 (m-80) REVERT: P 328 MET cc_start: 0.7683 (tpp) cc_final: 0.7369 (mmm) REVERT: Q 128 PHE cc_start: 0.8328 (m-80) cc_final: 0.7649 (m-10) REVERT: R 61 ILE cc_start: 0.6060 (OUTLIER) cc_final: 0.5284 (mp) REVERT: R 106 TYR cc_start: 0.8856 (m-80) cc_final: 0.7966 (m-80) REVERT: S 40 ARG cc_start: 0.8766 (mtt180) cc_final: 0.8538 (mtm-85) REVERT: S 91 MET cc_start: 0.8385 (tpt) cc_final: 0.8162 (mmm) REVERT: T 108 LEU cc_start: 0.8012 (mt) cc_final: 0.7326 (mt) REVERT: T 120 MET cc_start: 0.9071 (tpp) cc_final: 0.8553 (tpp) REVERT: W 36 ARG cc_start: 0.9188 (mtt90) cc_final: 0.8728 (mtt90) REVERT: W 45 GLU cc_start: 0.8460 (tp30) cc_final: 0.8224 (tm-30) REVERT: W 49 THR cc_start: 0.9574 (p) cc_final: 0.8918 (p) REVERT: W 73 ASN cc_start: 0.8810 (m-40) cc_final: 0.8574 (m110) REVERT: W 110 PHE cc_start: 0.8113 (m-80) cc_final: 0.7635 (m-80) REVERT: X 82 PHE cc_start: 0.8414 (t80) cc_final: 0.8182 (t80) REVERT: X 91 TYR cc_start: 0.7332 (t80) cc_final: 0.6576 (t80) REVERT: Z 65 LEU cc_start: 0.9088 (mt) cc_final: 0.8804 (mt) REVERT: a 53 ARG cc_start: 0.8451 (mtm110) cc_final: 0.7998 (ttt-90) REVERT: b 32 MET cc_start: 0.8969 (mmp) cc_final: 0.8648 (mmm) REVERT: b 43 SER cc_start: 0.8111 (t) cc_final: 0.7522 (m) REVERT: b 44 MET cc_start: 0.8391 (mtp) cc_final: 0.7414 (ptp) REVERT: b 51 TYR cc_start: 0.7952 (m-80) cc_final: 0.6888 (t80) REVERT: q 35 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6995 (mm) REVERT: q 68 MET cc_start: 0.6307 (ppp) cc_final: 0.5968 (ppp) REVERT: r 96 THR cc_start: 0.9212 (p) cc_final: 0.8817 (t) REVERT: r 101 MET cc_start: 0.8102 (ttp) cc_final: 0.7788 (ttm) REVERT: r 110 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: s 87 LEU cc_start: 0.7052 (pp) cc_final: 0.6745 (pp) outliers start: 145 outliers final: 60 residues processed: 1212 average time/residue: 0.2006 time to fit residues: 396.5524 Evaluate side-chains 949 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 880 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 168 ASN Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 435 VAL Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 636 TYR Chi-restraints excluded: chain G residue 704 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 60 ASP Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain W residue 71 MET Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Chi-restraints excluded: chain r residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 134 optimal weight: 8.9990 chunk 307 optimal weight: 8.9990 chunk 336 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 346 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 318 optimal weight: 30.0000 chunk 228 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 HIS ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 571 HIS H 235 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 215 ASN P 251 ASN P 275 HIS ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 ASN S 81 ASN V 83 GLN V 111 GLN W 129 HIS X 73 GLN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN b 52 ASN b 69 HIS q 17 HIS q 72 ASN r 110 GLN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.102368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.079635 restraints weight = 103234.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.082624 restraints weight = 48947.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.084580 restraints weight = 27439.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.084411 restraints weight = 23397.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.084512 restraints weight = 21191.117| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 34767 Z= 0.315 Angle : 1.080 76.669 47131 Z= 0.438 Chirality : 0.051 0.263 5134 Planarity : 0.006 0.130 5962 Dihedral : 9.809 179.224 4936 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 5.28 % Allowed : 19.84 % Favored : 74.88 % 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: -0.71 (0.13), residues: 4121 helix: 0.35 (0.12), residues: 1906 sheet: -1.00 (0.27), residues: 368 loop : -1.16 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 98 TYR 0.033 0.003 TYR B 170 PHE 0.033 0.003 PHE G 462 TRP 0.038 0.003 TRP r 104 HIS 0.035 0.002 HIS S 48 Details of bonding type rmsd covalent geometry : bond 0.00699 (34726) covalent geometry : angle 0.84604 (47039) SS BOND : bond 0.00273 ( 4) SS BOND : angle 0.69114 ( 8) hydrogen bonds : bond 0.05306 ( 1411) hydrogen bonds : angle 5.57598 ( 4116) metal coordination : bond 0.03948 ( 37) metal coordination : angle 15.90690 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 882 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9477 (mt) cc_final: 0.9258 (mt) REVERT: B 94 THR cc_start: 0.8562 (t) cc_final: 0.8344 (p) REVERT: B 112 TYR cc_start: 0.7599 (m-80) cc_final: 0.7381 (m-80) REVERT: B 122 ARG cc_start: 0.8949 (pmt170) cc_final: 0.8690 (pmt-80) REVERT: B 147 LYS cc_start: 0.8975 (mttt) cc_final: 0.8543 (ttpt) REVERT: B 152 MET cc_start: 0.8833 (mmm) cc_final: 0.8514 (mmm) REVERT: B 157 TYR cc_start: 0.8565 (m-80) cc_final: 0.8170 (m-80) REVERT: B 173 TYR cc_start: 0.8790 (m-80) cc_final: 0.8464 (m-80) REVERT: C 53 THR cc_start: 0.9621 (m) cc_final: 0.9374 (p) REVERT: C 227 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8497 (tm-30) REVERT: D 197 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8375 (ptm) REVERT: D 205 GLU cc_start: 0.8240 (tp30) cc_final: 0.7602 (tp30) REVERT: D 292 MET cc_start: 0.8657 (tpp) cc_final: 0.8403 (mmm) REVERT: D 296 SER cc_start: 0.8969 (m) cc_final: 0.8513 (t) REVERT: D 300 TRP cc_start: 0.8754 (t-100) cc_final: 0.8315 (t-100) REVERT: D 443 MET cc_start: 0.8864 (mpp) cc_final: 0.8316 (mpp) REVERT: D 461 ILE cc_start: 0.9464 (mp) cc_final: 0.9189 (mt) REVERT: E 58 ASN cc_start: 0.8710 (m-40) cc_final: 0.8449 (m-40) REVERT: E 98 ASN cc_start: 0.9012 (m-40) cc_final: 0.8582 (m110) REVERT: E 113 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7109 (mt-10) REVERT: E 124 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8127 (ttpt) REVERT: E 180 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7360 (p) REVERT: E 181 ASN cc_start: 0.7916 (m-40) cc_final: 0.7561 (t0) REVERT: E 184 MET cc_start: 0.8087 (ttm) cc_final: 0.7774 (ptm) REVERT: E 191 TYR cc_start: 0.6470 (m-80) cc_final: 0.5754 (m-80) REVERT: F 77 LEU cc_start: 0.9079 (tt) cc_final: 0.8767 (pp) REVERT: F 124 THR cc_start: 0.8527 (m) cc_final: 0.8040 (p) REVERT: F 300 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9086 (tp) REVERT: F 413 TRP cc_start: 0.8365 (t60) cc_final: 0.8033 (t60) REVERT: G 77 MET cc_start: 0.8864 (tpp) cc_final: 0.8508 (tpp) REVERT: G 94 MET cc_start: 0.8785 (tpt) cc_final: 0.8256 (tpp) REVERT: G 126 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8847 (pp) REVERT: G 138 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8061 (t0) REVERT: G 264 SER cc_start: 0.9277 (m) cc_final: 0.8845 (p) REVERT: G 396 GLU cc_start: 0.8273 (tt0) cc_final: 0.7931 (tp30) REVERT: G 605 GLN cc_start: 0.7956 (pp30) cc_final: 0.7534 (pp30) REVERT: G 618 GLU cc_start: 0.8623 (mp0) cc_final: 0.8306 (mp0) REVERT: G 707 MET cc_start: 0.9415 (mmm) cc_final: 0.9184 (mmm) REVERT: H 43 TYR cc_start: 0.8920 (m-80) cc_final: 0.8382 (m-10) REVERT: H 96 ILE cc_start: 0.8793 (mm) cc_final: 0.8512 (mm) REVERT: H 134 ARG cc_start: 0.8699 (ptm160) cc_final: 0.8084 (ptm160) REVERT: H 172 MET cc_start: 0.7560 (ppp) cc_final: 0.7101 (ppp) REVERT: H 173 TRP cc_start: 0.8246 (m-10) cc_final: 0.7635 (m-90) REVERT: H 181 MET cc_start: 0.8928 (mtt) cc_final: 0.8377 (mtt) REVERT: H 183 MET cc_start: 0.9202 (mtp) cc_final: 0.8930 (mtp) REVERT: H 200 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8440 (pp) REVERT: H 234 MET cc_start: 0.9200 (mmm) cc_final: 0.8961 (mmm) REVERT: H 247 TYR cc_start: 0.8144 (t80) cc_final: 0.7878 (t80) REVERT: H 268 SER cc_start: 0.9396 (m) cc_final: 0.9071 (t) REVERT: H 282 TYR cc_start: 0.8010 (t80) cc_final: 0.7547 (t80) REVERT: H 286 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8485 (mpp) REVERT: H 292 ASN cc_start: 0.8347 (m-40) cc_final: 0.8033 (m-40) REVERT: I 42 LYS cc_start: 0.6776 (mmtt) cc_final: 0.6259 (tptt) REVERT: I 63 TRP cc_start: 0.8970 (m-10) cc_final: 0.8718 (m-10) REVERT: I 191 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8514 (tt) REVERT: I 204 ASN cc_start: 0.9041 (m110) cc_final: 0.8678 (m-40) REVERT: I 208 ASP cc_start: 0.8334 (t0) cc_final: 0.7888 (t70) REVERT: Q 78 ARG cc_start: 0.8536 (ptm-80) cc_final: 0.8314 (ptm-80) REVERT: Q 99 MET cc_start: 0.8989 (ptp) cc_final: 0.8689 (ptp) REVERT: Q 105 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6460 (tt0) REVERT: Q 107 TRP cc_start: 0.8504 (p90) cc_final: 0.8268 (p90) REVERT: Q 128 PHE cc_start: 0.8682 (m-80) cc_final: 0.7803 (m-10) REVERT: Q 145 TYR cc_start: 0.9217 (p90) cc_final: 0.8847 (p90) REVERT: R 106 TYR cc_start: 0.9154 (m-80) cc_final: 0.8819 (m-80) REVERT: S 40 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8107 (mtm-85) REVERT: S 45 LYS cc_start: 0.9173 (tptt) cc_final: 0.8745 (mmmt) REVERT: S 57 GLU cc_start: 0.7037 (pm20) cc_final: 0.6832 (pm20) REVERT: T 80 LYS cc_start: 0.8924 (mttt) cc_final: 0.8624 (mmtt) REVERT: T 119 ILE cc_start: 0.9347 (mm) cc_final: 0.9040 (mm) REVERT: T 139 MET cc_start: 0.8393 (ttm) cc_final: 0.7992 (ttm) REVERT: V 97 TRP cc_start: 0.8147 (m-10) cc_final: 0.7753 (m-10) REVERT: W 45 GLU cc_start: 0.8534 (tp30) cc_final: 0.7920 (tp30) REVERT: W 56 ASP cc_start: 0.8887 (t0) cc_final: 0.8646 (t0) REVERT: W 87 ILE cc_start: 0.9683 (mm) cc_final: 0.9421 (mm) REVERT: W 95 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8599 (mt-10) REVERT: W 120 ASP cc_start: 0.8714 (t0) cc_final: 0.8468 (t0) REVERT: W 129 HIS cc_start: 0.7462 (m90) cc_final: 0.7033 (m-70) REVERT: Z 65 LEU cc_start: 0.9238 (mt) cc_final: 0.8960 (mt) REVERT: a 53 ARG cc_start: 0.8557 (mtm110) cc_final: 0.7977 (ttt-90) REVERT: b 15 LYS cc_start: 0.9011 (pttp) cc_final: 0.8679 (mmtm) REVERT: b 32 MET cc_start: 0.9011 (mmp) cc_final: 0.8770 (mmm) REVERT: b 51 TYR cc_start: 0.8327 (m-80) cc_final: 0.7069 (t80) REVERT: s 87 LEU cc_start: 0.7326 (pp) cc_final: 0.6990 (pp) outliers start: 191 outliers final: 110 residues processed: 997 average time/residue: 0.1999 time to fit residues: 326.9753 Evaluate side-chains 920 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 800 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 435 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 284 GLU Chi-restraints excluded: chain G residue 584 LEU Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 649 VAL Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 665 PHE Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 154 LYS Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 128 SER Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 378 optimal weight: 0.8980 chunk 389 optimal weight: 20.0000 chunk 157 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 358 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 308 optimal weight: 30.0000 chunk 366 optimal weight: 0.5980 chunk 191 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 123 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 258 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 GLN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 HIS T 101 ASN V 83 GLN W 73 ASN a 31 ASN q 31 ASN r 110 GLN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.106519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.086304 restraints weight = 101993.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.087609 restraints weight = 43945.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088823 restraints weight = 30309.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088705 restraints weight = 24893.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.089218 restraints weight = 24069.545| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34767 Z= 0.158 Angle : 0.950 77.079 47131 Z= 0.375 Chirality : 0.046 0.291 5134 Planarity : 0.005 0.128 5962 Dihedral : 9.503 179.849 4936 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.17 % Rotamer: Outliers : 4.20 % Allowed : 21.80 % Favored : 74.00 % 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: -0.48 (0.13), residues: 4121 helix: 0.55 (0.12), residues: 1881 sheet: -0.85 (0.27), residues: 371 loop : -1.04 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG q 34 TYR 0.028 0.002 TYR Q 160 PHE 0.031 0.002 PHE X 82 TRP 0.039 0.002 TRP F 62 HIS 0.010 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00365 (34726) covalent geometry : angle 0.74271 (47039) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.47283 ( 8) hydrogen bonds : bond 0.04488 ( 1411) hydrogen bonds : angle 5.16010 ( 4116) metal coordination : bond 0.01676 ( 37) metal coordination : angle 14.04430 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 939 time to evaluate : 1.153 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: A 53 MET cc_start: 0.8275 (mpp) cc_final: 0.7497 (tpp) REVERT: B 94 THR cc_start: 0.8444 (t) cc_final: 0.7944 (p) REVERT: B 103 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 104 MET cc_start: 0.8855 (ttt) cc_final: 0.8505 (ttt) REVERT: B 122 ARG cc_start: 0.8816 (pmt170) cc_final: 0.8260 (ttt180) REVERT: B 147 LYS cc_start: 0.8925 (mttt) cc_final: 0.8374 (ttpt) REVERT: B 157 TYR cc_start: 0.8377 (m-80) cc_final: 0.8056 (m-80) REVERT: B 173 TYR cc_start: 0.8754 (m-80) cc_final: 0.8298 (m-80) REVERT: C 114 THR cc_start: 0.9341 (t) cc_final: 0.9062 (p) REVERT: C 216 LYS cc_start: 0.9268 (mmtt) cc_final: 0.8896 (mmtt) REVERT: C 227 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: D 197 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7329 (ptm) REVERT: D 205 GLU cc_start: 0.7971 (tp30) cc_final: 0.7534 (tp30) REVERT: D 296 SER cc_start: 0.8899 (m) cc_final: 0.8427 (t) REVERT: D 443 MET cc_start: 0.8671 (mpp) cc_final: 0.8274 (mpp) REVERT: E 105 GLN cc_start: 0.8994 (pt0) cc_final: 0.8572 (pm20) REVERT: E 113 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7051 (mt-10) REVERT: E 180 VAL cc_start: 0.7548 (OUTLIER) cc_final: 0.7331 (p) REVERT: E 181 ASN cc_start: 0.8028 (m-40) cc_final: 0.7440 (t0) REVERT: E 184 MET cc_start: 0.7883 (ttm) cc_final: 0.7630 (ptp) REVERT: F 77 LEU cc_start: 0.9045 (tt) cc_final: 0.8787 (pp) REVERT: F 209 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8061 (mp0) REVERT: F 276 PHE cc_start: 0.6568 (m-80) cc_final: 0.6215 (m-10) REVERT: G 77 MET cc_start: 0.8885 (tpp) cc_final: 0.8538 (tpp) REVERT: G 94 MET cc_start: 0.8768 (tpt) cc_final: 0.8319 (tpp) REVERT: G 97 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5440 (mtm) REVERT: G 138 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7924 (t0) REVERT: G 264 SER cc_start: 0.9224 (m) cc_final: 0.8872 (p) REVERT: G 396 GLU cc_start: 0.8172 (tt0) cc_final: 0.7851 (tp30) REVERT: G 605 GLN cc_start: 0.7908 (pp30) cc_final: 0.7459 (pp30) REVERT: G 608 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8541 (m) REVERT: G 618 GLU cc_start: 0.8721 (mp0) cc_final: 0.8364 (mp0) REVERT: G 670 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8949 (mm-30) REVERT: G 707 MET cc_start: 0.9314 (mmm) cc_final: 0.9055 (mmm) REVERT: H 15 ILE cc_start: 0.9163 (mm) cc_final: 0.8913 (mt) REVERT: H 32 GLN cc_start: 0.8739 (mt0) cc_final: 0.8264 (mt0) REVERT: H 43 TYR cc_start: 0.8707 (m-80) cc_final: 0.8164 (m-10) REVERT: H 54 LYS cc_start: 0.9189 (ptmm) cc_final: 0.8947 (ptmm) REVERT: H 86 TRP cc_start: 0.8660 (m100) cc_final: 0.8257 (m100) REVERT: H 173 TRP cc_start: 0.8144 (m-10) cc_final: 0.7653 (m-90) REVERT: H 181 MET cc_start: 0.8796 (mtt) cc_final: 0.8267 (mtt) REVERT: H 234 MET cc_start: 0.9143 (mmm) cc_final: 0.8780 (mmm) REVERT: H 247 TYR cc_start: 0.8075 (t80) cc_final: 0.7801 (t80) REVERT: H 282 TYR cc_start: 0.7760 (t80) cc_final: 0.7125 (t80) REVERT: H 286 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8516 (mpp) REVERT: H 292 ASN cc_start: 0.8211 (m-40) cc_final: 0.7914 (m-40) REVERT: H 302 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8383 (ttp) REVERT: I 63 TRP cc_start: 0.8895 (m-10) cc_final: 0.8617 (m-10) REVERT: I 76 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7458 (t80) REVERT: I 94 SER cc_start: 0.8720 (p) cc_final: 0.8469 (p) REVERT: I 98 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7292 (mtt90) REVERT: I 208 ASP cc_start: 0.8160 (t0) cc_final: 0.7765 (t70) REVERT: P 283 MET cc_start: 0.7845 (mmp) cc_final: 0.6077 (tpp) REVERT: Q 78 ARG cc_start: 0.8586 (ptm-80) cc_final: 0.8372 (ptm-80) REVERT: Q 105 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6478 (tt0) REVERT: Q 128 PHE cc_start: 0.8665 (m-80) cc_final: 0.7994 (m-10) REVERT: R 45 ARG cc_start: 0.2495 (ptt180) cc_final: 0.1756 (tmm-80) REVERT: R 73 GLU cc_start: 0.8231 (pm20) cc_final: 0.7267 (mp0) REVERT: R 80 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7558 (t0) REVERT: R 106 TYR cc_start: 0.9127 (m-80) cc_final: 0.8870 (m-80) REVERT: S 40 ARG cc_start: 0.9045 (mtt180) cc_final: 0.8708 (mtm-85) REVERT: S 45 LYS cc_start: 0.9069 (tptt) cc_final: 0.8645 (mmmt) REVERT: T 80 LYS cc_start: 0.8834 (mttt) cc_final: 0.8490 (mmtt) REVERT: T 124 ASP cc_start: 0.8413 (m-30) cc_final: 0.8150 (t0) REVERT: T 138 LEU cc_start: 0.9222 (tp) cc_final: 0.8930 (tp) REVERT: V 83 GLN cc_start: 0.8474 (tp-100) cc_final: 0.8170 (tp40) REVERT: V 97 TRP cc_start: 0.7858 (m-10) cc_final: 0.7597 (m-10) REVERT: W 45 GLU cc_start: 0.8583 (tp30) cc_final: 0.8089 (tp30) REVERT: W 56 ASP cc_start: 0.8243 (t0) cc_final: 0.7552 (t0) REVERT: W 83 ASP cc_start: 0.7865 (t0) cc_final: 0.7398 (t0) REVERT: W 91 MET cc_start: 0.8454 (mtt) cc_final: 0.8210 (mtt) REVERT: W 95 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8440 (mt-10) REVERT: W 129 HIS cc_start: 0.7360 (m90) cc_final: 0.6841 (m-70) REVERT: X 43 PHE cc_start: 0.7965 (t80) cc_final: 0.7682 (t80) REVERT: Z 65 LEU cc_start: 0.9238 (mt) cc_final: 0.8939 (mt) REVERT: a 53 ARG cc_start: 0.8516 (mtm110) cc_final: 0.7942 (ttt-90) REVERT: b 15 LYS cc_start: 0.8922 (pttp) cc_final: 0.8601 (mmtm) REVERT: b 26 TRP cc_start: 0.7931 (t60) cc_final: 0.7690 (t60) REVERT: b 32 MET cc_start: 0.8971 (mmp) cc_final: 0.8761 (mmm) REVERT: b 51 TYR cc_start: 0.8096 (m-80) cc_final: 0.7088 (t80) REVERT: b 52 ASN cc_start: 0.7509 (t0) cc_final: 0.6773 (m110) REVERT: b 53 TYR cc_start: 0.8524 (t80) cc_final: 0.7859 (t80) REVERT: q 68 MET cc_start: 0.6311 (ppp) cc_final: 0.6089 (ppp) REVERT: q 127 TYR cc_start: 0.6704 (p90) cc_final: 0.6336 (p90) REVERT: s 87 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7109 (pp) outliers start: 152 outliers final: 78 residues processed: 1028 average time/residue: 0.2077 time to fit residues: 349.8399 Evaluate side-chains 922 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 832 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 665 PHE Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 154 LYS Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 89 LEU Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 17 HIS Chi-restraints excluded: chain q residue 128 SER Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU Chi-restraints excluded: chain s residue 82 ASP Chi-restraints excluded: chain s residue 87 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 373 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 353 optimal weight: 1.9990 chunk 385 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 196 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 104 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 HIS E 68 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 215 ASN P 269 ASN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN T 101 ASN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 ASN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.104755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080792 restraints weight = 104327.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083636 restraints weight = 49509.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085441 restraints weight = 31415.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.086537 restraints weight = 23831.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.087200 restraints weight = 20268.690| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34767 Z= 0.181 Angle : 0.958 78.821 47131 Z= 0.372 Chirality : 0.047 0.264 5134 Planarity : 0.005 0.129 5962 Dihedral : 9.311 159.511 4936 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer: Outliers : 3.92 % Allowed : 23.51 % Favored : 72.56 % 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: -0.39 (0.13), residues: 4121 helix: 0.59 (0.12), residues: 1894 sheet: -0.86 (0.27), residues: 383 loop : -0.95 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG r 27 TYR 0.016 0.002 TYR D 214 PHE 0.032 0.002 PHE W 121 TRP 0.059 0.002 TRP F 62 HIS 0.011 0.002 HIS P 122 Details of bonding type rmsd covalent geometry : bond 0.00418 (34726) covalent geometry : angle 0.72983 (47039) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.42175 ( 8) hydrogen bonds : bond 0.04411 ( 1411) hydrogen bonds : angle 5.10795 ( 4116) metal coordination : bond 0.02103 ( 37) metal coordination : angle 14.72374 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 862 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 SER cc_start: 0.9067 (m) cc_final: 0.8846 (p) REVERT: A 53 MET cc_start: 0.8177 (mpp) cc_final: 0.7381 (tpp) REVERT: B 77 LYS cc_start: 0.9034 (mttt) cc_final: 0.8646 (mttm) REVERT: B 122 ARG cc_start: 0.8739 (pmt170) cc_final: 0.8327 (tpt170) REVERT: B 147 LYS cc_start: 0.8931 (mttt) cc_final: 0.8397 (ttpt) REVERT: B 157 TYR cc_start: 0.8430 (m-80) cc_final: 0.7901 (m-80) REVERT: B 173 TYR cc_start: 0.8745 (m-80) cc_final: 0.8364 (m-80) REVERT: B 199 GLU cc_start: 0.8157 (mp0) cc_final: 0.7747 (mp0) REVERT: B 220 ILE cc_start: 0.9187 (tp) cc_final: 0.8984 (tp) REVERT: C 114 THR cc_start: 0.9333 (t) cc_final: 0.8995 (p) REVERT: C 166 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8447 (tt0) REVERT: C 207 VAL cc_start: 0.9542 (m) cc_final: 0.9338 (p) REVERT: C 227 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: D 105 MET cc_start: 0.7231 (tmm) cc_final: 0.6893 (tpp) REVERT: D 197 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8117 (ptm) REVERT: D 205 GLU cc_start: 0.7954 (tp30) cc_final: 0.7253 (tp30) REVERT: D 296 SER cc_start: 0.8932 (m) cc_final: 0.8664 (t) REVERT: D 351 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7894 (ttp) REVERT: D 443 MET cc_start: 0.8626 (mpp) cc_final: 0.7939 (mpp) REVERT: E 105 GLN cc_start: 0.9022 (pt0) cc_final: 0.8656 (pm20) REVERT: E 113 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7438 (mt-10) REVERT: E 181 ASN cc_start: 0.7987 (m-40) cc_final: 0.7332 (t0) REVERT: E 184 MET cc_start: 0.8023 (ttm) cc_final: 0.7271 (ptp) REVERT: F 209 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8011 (mp0) REVERT: G 94 MET cc_start: 0.8715 (tpt) cc_final: 0.8381 (tpp) REVERT: G 97 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5511 (mtm) REVERT: G 126 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8832 (pp) REVERT: G 138 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8039 (t0) REVERT: G 264 SER cc_start: 0.9318 (m) cc_final: 0.8873 (p) REVERT: G 396 GLU cc_start: 0.8115 (tt0) cc_final: 0.7720 (tp30) REVERT: G 605 GLN cc_start: 0.7950 (pp30) cc_final: 0.7579 (pp30) REVERT: G 608 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8595 (m) REVERT: G 618 GLU cc_start: 0.8702 (mp0) cc_final: 0.8361 (mp0) REVERT: G 707 MET cc_start: 0.9327 (mmm) cc_final: 0.9093 (mmm) REVERT: H 15 ILE cc_start: 0.9206 (mm) cc_final: 0.8982 (mt) REVERT: H 54 LYS cc_start: 0.9263 (ptmm) cc_final: 0.8808 (ptmm) REVERT: H 58 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8785 (ttmm) REVERT: H 86 TRP cc_start: 0.8703 (m100) cc_final: 0.8381 (m100) REVERT: H 134 ARG cc_start: 0.8536 (ptm160) cc_final: 0.8192 (ptp-170) REVERT: H 173 TRP cc_start: 0.8206 (m-10) cc_final: 0.7660 (m-90) REVERT: H 181 MET cc_start: 0.8897 (mtt) cc_final: 0.8349 (mtt) REVERT: H 224 PHE cc_start: 0.8505 (t80) cc_final: 0.7800 (t80) REVERT: H 234 MET cc_start: 0.9193 (mmm) cc_final: 0.8837 (mmm) REVERT: H 247 TYR cc_start: 0.8115 (t80) cc_final: 0.7821 (t80) REVERT: H 282 TYR cc_start: 0.7848 (t80) cc_final: 0.7219 (t80) REVERT: H 286 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8408 (mpp) REVERT: H 292 ASN cc_start: 0.8351 (m-40) cc_final: 0.8087 (m-40) REVERT: I 63 TRP cc_start: 0.8953 (m-10) cc_final: 0.8711 (m-90) REVERT: I 76 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7696 (t80) REVERT: I 94 SER cc_start: 0.8563 (p) cc_final: 0.8273 (p) REVERT: I 191 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8582 (tt) REVERT: I 208 ASP cc_start: 0.8335 (t0) cc_final: 0.7883 (t70) REVERT: P 79 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8606 (mt0) REVERT: P 210 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7810 (tp30) REVERT: P 283 MET cc_start: 0.7954 (mmp) cc_final: 0.6328 (tpp) REVERT: P 298 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7219 (t80) REVERT: P 328 MET cc_start: 0.7448 (mmm) cc_final: 0.7221 (mmm) REVERT: Q 78 ARG cc_start: 0.8528 (ptm-80) cc_final: 0.8281 (ptm-80) REVERT: Q 96 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8474 (mttp) REVERT: Q 99 MET cc_start: 0.9020 (ptp) cc_final: 0.8627 (ptp) REVERT: Q 105 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6588 (tt0) REVERT: Q 128 PHE cc_start: 0.8717 (m-80) cc_final: 0.7847 (m-10) REVERT: R 80 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7673 (t0) REVERT: R 106 TYR cc_start: 0.9131 (m-80) cc_final: 0.8915 (m-80) REVERT: S 40 ARG cc_start: 0.9072 (mtt180) cc_final: 0.8704 (mtm180) REVERT: S 45 LYS cc_start: 0.9130 (tptt) cc_final: 0.8862 (mmmt) REVERT: T 80 LYS cc_start: 0.8983 (mttt) cc_final: 0.8760 (tmtt) REVERT: T 115 GLN cc_start: 0.8743 (tt0) cc_final: 0.8486 (mt0) REVERT: W 24 PHE cc_start: 0.8649 (m-80) cc_final: 0.8438 (m-80) REVERT: W 45 GLU cc_start: 0.8645 (tp30) cc_final: 0.8021 (tp30) REVERT: W 61 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8675 (mm-40) REVERT: W 91 MET cc_start: 0.8510 (mtt) cc_final: 0.8197 (mtt) REVERT: W 92 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8318 (mm-30) REVERT: W 95 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8266 (mt-10) REVERT: W 129 HIS cc_start: 0.7311 (m90) cc_final: 0.6889 (m-70) REVERT: Z 22 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7489 (mmtt) REVERT: Z 65 LEU cc_start: 0.9377 (mt) cc_final: 0.9113 (mt) REVERT: a 53 ARG cc_start: 0.8417 (mtm110) cc_final: 0.7874 (ttt-90) REVERT: b 15 LYS cc_start: 0.8906 (pttp) cc_final: 0.8593 (mmtm) REVERT: b 51 TYR cc_start: 0.8097 (m-80) cc_final: 0.7102 (t80) REVERT: q 58 ARG cc_start: 0.7051 (ttt180) cc_final: 0.6058 (ttt180) REVERT: q 68 MET cc_start: 0.6360 (ppp) cc_final: 0.6069 (ppp) outliers start: 142 outliers final: 85 residues processed: 938 average time/residue: 0.2051 time to fit residues: 317.8758 Evaluate side-chains 902 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 803 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 543 LYS Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 665 PHE Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 96 LYS Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 154 LYS Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 22 LYS Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 17 HIS Chi-restraints excluded: chain q residue 128 SER Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 214 optimal weight: 6.9990 chunk 379 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 258 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 ASN T 101 ASN V 83 GLN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 ASN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.103933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083248 restraints weight = 102523.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.084864 restraints weight = 44091.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085841 restraints weight = 30037.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.085783 restraints weight = 24831.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.085882 restraints weight = 23745.070| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 34767 Z= 0.200 Angle : 0.979 81.720 47131 Z= 0.378 Chirality : 0.047 0.238 5134 Planarity : 0.005 0.131 5962 Dihedral : 9.229 145.581 4936 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.83 % Rotamer: Outliers : 4.03 % Allowed : 24.68 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4121 helix: 0.67 (0.12), residues: 1890 sheet: -0.87 (0.27), residues: 388 loop : -0.93 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 107 TYR 0.020 0.002 TYR D 214 PHE 0.026 0.002 PHE A 92 TRP 0.066 0.002 TRP F 62 HIS 0.017 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00460 (34726) covalent geometry : angle 0.74768 (47039) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.47233 ( 8) hydrogen bonds : bond 0.04327 ( 1411) hydrogen bonds : angle 5.09310 ( 4116) metal coordination : bond 0.02416 ( 37) metal coordination : angle 14.98874 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 846 time to evaluate : 1.291 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: A 53 MET cc_start: 0.8382 (mpp) cc_final: 0.7589 (tpp) REVERT: A 83 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8274 (mmtt) REVERT: B 103 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7968 (tp30) REVERT: B 122 ARG cc_start: 0.8691 (pmt170) cc_final: 0.8319 (ttt180) REVERT: B 147 LYS cc_start: 0.8935 (mttt) cc_final: 0.8389 (ttpt) REVERT: B 157 TYR cc_start: 0.8490 (m-80) cc_final: 0.7980 (m-80) REVERT: B 173 TYR cc_start: 0.8825 (m-80) cc_final: 0.8537 (m-80) REVERT: B 220 ILE cc_start: 0.9139 (tp) cc_final: 0.8938 (tp) REVERT: C 207 VAL cc_start: 0.9595 (m) cc_final: 0.9371 (p) REVERT: C 227 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8479 (tm-30) REVERT: D 105 MET cc_start: 0.8015 (tmm) cc_final: 0.7553 (tpt) REVERT: D 197 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8176 (ptm) REVERT: D 205 GLU cc_start: 0.8130 (tp30) cc_final: 0.7573 (tp30) REVERT: D 296 SER cc_start: 0.8997 (m) cc_final: 0.8720 (t) REVERT: E 58 ASN cc_start: 0.9007 (m-40) cc_final: 0.8784 (m-40) REVERT: E 105 GLN cc_start: 0.9040 (pt0) cc_final: 0.8691 (pm20) REVERT: E 113 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7588 (mt-10) REVERT: E 124 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7713 (ttpt) REVERT: E 180 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7296 (p) REVERT: E 181 ASN cc_start: 0.7841 (m-40) cc_final: 0.7240 (t0) REVERT: F 131 MET cc_start: 0.8245 (ptm) cc_final: 0.7804 (ppp) REVERT: F 209 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8068 (mp0) REVERT: F 276 PHE cc_start: 0.6577 (m-10) cc_final: 0.6374 (m-10) REVERT: G 94 MET cc_start: 0.8704 (tpt) cc_final: 0.8378 (tpp) REVERT: G 97 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5829 (mtm) REVERT: G 136 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7544 (tt0) REVERT: G 138 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (t0) REVERT: G 264 SER cc_start: 0.9334 (m) cc_final: 0.8894 (p) REVERT: G 306 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7912 (ttm) REVERT: G 396 GLU cc_start: 0.8173 (tt0) cc_final: 0.7759 (tp30) REVERT: G 544 MET cc_start: 0.9178 (tpp) cc_final: 0.8968 (tpp) REVERT: G 605 GLN cc_start: 0.7986 (pp30) cc_final: 0.7603 (pp30) REVERT: G 608 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8608 (m) REVERT: G 618 GLU cc_start: 0.8732 (mp0) cc_final: 0.8315 (mp0) REVERT: G 707 MET cc_start: 0.9357 (mmm) cc_final: 0.9131 (mmm) REVERT: H 15 ILE cc_start: 0.9235 (mm) cc_final: 0.9019 (mt) REVERT: H 54 LYS cc_start: 0.9279 (ptmm) cc_final: 0.8607 (ptmt) REVERT: H 134 ARG cc_start: 0.8637 (ptm160) cc_final: 0.8389 (ptp-170) REVERT: H 173 TRP cc_start: 0.8241 (m-10) cc_final: 0.7730 (m-90) REVERT: H 181 MET cc_start: 0.8884 (mtt) cc_final: 0.8451 (mtt) REVERT: H 224 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7787 (t80) REVERT: H 225 MET cc_start: 0.9071 (mmt) cc_final: 0.8623 (mmt) REVERT: H 234 MET cc_start: 0.9177 (mmm) cc_final: 0.8792 (mmm) REVERT: H 247 TYR cc_start: 0.8124 (t80) cc_final: 0.7814 (t80) REVERT: H 282 TYR cc_start: 0.7856 (t80) cc_final: 0.7123 (t80) REVERT: H 286 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8368 (mpp) REVERT: H 292 ASN cc_start: 0.8445 (m-40) cc_final: 0.8130 (m-40) REVERT: I 63 TRP cc_start: 0.8981 (m-10) cc_final: 0.8679 (m-90) REVERT: I 73 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8165 (t) REVERT: I 76 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7716 (t80) REVERT: I 98 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7395 (mtm-85) REVERT: I 117 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8879 (mtpp) REVERT: I 191 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8645 (tt) REVERT: I 208 ASP cc_start: 0.8452 (t0) cc_final: 0.8085 (t70) REVERT: P 79 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8541 (mt0) REVERT: P 97 MET cc_start: 0.7871 (ptp) cc_final: 0.7648 (ptp) REVERT: P 210 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7564 (tp30) REVERT: P 283 MET cc_start: 0.8054 (mmp) cc_final: 0.6389 (tpp) REVERT: P 298 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7240 (t80) REVERT: P 351 GLU cc_start: 0.8250 (mp0) cc_final: 0.7818 (mp0) REVERT: Q 78 ARG cc_start: 0.8583 (ptm-80) cc_final: 0.8319 (ptm-80) REVERT: Q 96 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8431 (mttp) REVERT: Q 105 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6751 (tt0) REVERT: Q 128 PHE cc_start: 0.8860 (m-80) cc_final: 0.8521 (m-80) REVERT: R 73 GLU cc_start: 0.8308 (pm20) cc_final: 0.7243 (mp0) REVERT: R 80 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7785 (t0) REVERT: S 40 ARG cc_start: 0.9136 (mtt180) cc_final: 0.8734 (mtm180) REVERT: S 45 LYS cc_start: 0.9153 (tptt) cc_final: 0.8900 (mmmt) REVERT: S 62 GLN cc_start: 0.8808 (mp10) cc_final: 0.8508 (mp10) REVERT: T 80 LYS cc_start: 0.8975 (mttt) cc_final: 0.8764 (tmtt) REVERT: T 117 GLU cc_start: 0.7719 (pp20) cc_final: 0.7469 (pp20) REVERT: T 118 ILE cc_start: 0.8813 (mm) cc_final: 0.8601 (mm) REVERT: V 53 ASN cc_start: 0.8870 (m-40) cc_final: 0.8497 (m-40) REVERT: V 83 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7935 (tm-30) REVERT: W 24 PHE cc_start: 0.8740 (m-80) cc_final: 0.8442 (m-80) REVERT: W 45 GLU cc_start: 0.8659 (tp30) cc_final: 0.7945 (tp30) REVERT: W 56 ASP cc_start: 0.8638 (t0) cc_final: 0.8062 (t0) REVERT: W 91 MET cc_start: 0.8484 (mtt) cc_final: 0.8205 (mtt) REVERT: W 95 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8431 (mt-10) REVERT: W 109 PHE cc_start: 0.8810 (m-80) cc_final: 0.8519 (m-80) REVERT: W 129 HIS cc_start: 0.7473 (m90) cc_final: 0.7205 (m-70) REVERT: X 32 TYR cc_start: 0.8500 (t80) cc_final: 0.8250 (t80) REVERT: X 44 MET cc_start: 0.9048 (tpp) cc_final: 0.8729 (mpp) REVERT: Z 51 MET cc_start: 0.8465 (tmm) cc_final: 0.8231 (tmm) REVERT: Z 65 LEU cc_start: 0.9402 (mt) cc_final: 0.9148 (mm) REVERT: a 48 MET cc_start: 0.8394 (mmm) cc_final: 0.8175 (mmm) REVERT: a 53 ARG cc_start: 0.8400 (mtm110) cc_final: 0.7872 (ttt-90) REVERT: b 15 LYS cc_start: 0.9005 (pttp) cc_final: 0.8715 (mmtm) REVERT: b 26 TRP cc_start: 0.7962 (t60) cc_final: 0.7686 (t60) REVERT: b 43 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7986 (m) REVERT: b 51 TYR cc_start: 0.8080 (m-80) cc_final: 0.7195 (t80) REVERT: q 42 ASP cc_start: 0.5665 (t70) cc_final: 0.5293 (t70) REVERT: q 77 VAL cc_start: 0.8254 (t) cc_final: 0.8025 (p) outliers start: 146 outliers final: 95 residues processed: 929 average time/residue: 0.2030 time to fit residues: 311.6425 Evaluate side-chains 909 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 795 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 543 LYS Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 584 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 665 PHE Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 96 LYS Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 154 LYS Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 54 GLN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain q residue 17 HIS Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 82 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 374 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 393 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 391 optimal weight: 20.0000 chunk 187 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 405 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 HIS ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 ASN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 ASN q 72 ASN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077290 restraints weight = 105655.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077869 restraints weight = 47662.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078854 restraints weight = 35116.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.079216 restraints weight = 28421.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.079634 restraints weight = 26576.666| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 34767 Z= 0.346 Angle : 1.137 84.501 47131 Z= 0.436 Chirality : 0.052 0.270 5134 Planarity : 0.006 0.135 5962 Dihedral : 9.230 124.736 4936 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 5.11 % Allowed : 24.70 % Favored : 70.19 % 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: -0.57 (0.13), residues: 4121 helix: 0.44 (0.12), residues: 1892 sheet: -1.02 (0.26), residues: 394 loop : -1.03 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 184 TYR 0.024 0.003 TYR D 286 PHE 0.025 0.003 PHE G 146 TRP 0.065 0.003 TRP F 62 HIS 0.015 0.002 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00777 (34726) covalent geometry : angle 0.85144 (47039) SS BOND : bond 0.00328 ( 4) SS BOND : angle 0.64318 ( 8) hydrogen bonds : bond 0.04780 ( 1411) hydrogen bonds : angle 5.40407 ( 4116) metal coordination : bond 0.04019 ( 37) metal coordination : angle 17.88212 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 791 time to evaluate : 1.376 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: B 103 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8188 (tp30) REVERT: B 113 ASP cc_start: 0.8331 (t0) cc_final: 0.8062 (t0) REVERT: B 122 ARG cc_start: 0.8744 (pmt170) cc_final: 0.8281 (tpt-90) REVERT: B 124 SER cc_start: 0.9157 (m) cc_final: 0.8524 (p) REVERT: B 127 GLN cc_start: 0.8832 (pm20) cc_final: 0.8379 (pm20) REVERT: B 131 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8311 (ttt) REVERT: B 147 LYS cc_start: 0.9009 (mttt) cc_final: 0.8432 (ttpt) REVERT: B 157 TYR cc_start: 0.8674 (m-80) cc_final: 0.8429 (m-80) REVERT: B 220 ILE cc_start: 0.9264 (tp) cc_final: 0.9055 (tp) REVERT: C 149 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9339 (pp) REVERT: C 227 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8734 (tm-30) REVERT: D 125 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8350 (mt-10) REVERT: D 197 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8392 (ptm) REVERT: D 205 GLU cc_start: 0.8284 (tp30) cc_final: 0.7818 (tp30) REVERT: D 296 SER cc_start: 0.9120 (m) cc_final: 0.8876 (t) REVERT: D 446 ASP cc_start: 0.8672 (m-30) cc_final: 0.8341 (m-30) REVERT: E 58 ASN cc_start: 0.9120 (m-40) cc_final: 0.8915 (m-40) REVERT: E 98 ASN cc_start: 0.9118 (m-40) cc_final: 0.8758 (m110) REVERT: E 105 GLN cc_start: 0.9106 (pt0) cc_final: 0.8834 (pm20) REVERT: E 113 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7527 (mt-10) REVERT: E 181 ASN cc_start: 0.8055 (m-40) cc_final: 0.7648 (t0) REVERT: E 194 ASP cc_start: 0.7329 (t0) cc_final: 0.6918 (t0) REVERT: E 205 ASP cc_start: 0.7882 (m-30) cc_final: 0.7630 (m-30) REVERT: F 377 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: F 413 TRP cc_start: 0.8428 (t60) cc_final: 0.8138 (t60) REVERT: G 94 MET cc_start: 0.8809 (tpt) cc_final: 0.8485 (tpp) REVERT: G 97 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5933 (mtm) REVERT: G 136 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8098 (tt0) REVERT: G 138 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7889 (t0) REVERT: G 264 SER cc_start: 0.9345 (m) cc_final: 0.8916 (p) REVERT: G 306 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8031 (mtm) REVERT: G 396 GLU cc_start: 0.8317 (tt0) cc_final: 0.7978 (tp30) REVERT: G 605 GLN cc_start: 0.8065 (pp30) cc_final: 0.7610 (pp30) REVERT: G 608 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8705 (m) REVERT: G 618 GLU cc_start: 0.8793 (mp0) cc_final: 0.8373 (mp0) REVERT: G 707 MET cc_start: 0.9428 (mmm) cc_final: 0.9198 (mmm) REVERT: H 15 ILE cc_start: 0.9360 (mm) cc_final: 0.9064 (mt) REVERT: H 54 LYS cc_start: 0.9300 (ptmm) cc_final: 0.8925 (ptmm) REVERT: H 134 ARG cc_start: 0.8841 (ptm160) cc_final: 0.8339 (ptp-170) REVERT: H 181 MET cc_start: 0.8934 (mtt) cc_final: 0.8551 (mtt) REVERT: H 225 MET cc_start: 0.9078 (mmt) cc_final: 0.8428 (mmt) REVERT: H 234 MET cc_start: 0.9255 (mmm) cc_final: 0.8499 (mmm) REVERT: H 282 TYR cc_start: 0.8157 (t80) cc_final: 0.7544 (t80) REVERT: H 286 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.8319 (mpp) REVERT: H 291 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8086 (mmmm) REVERT: H 292 ASN cc_start: 0.8328 (m-40) cc_final: 0.8037 (m-40) REVERT: I 63 TRP cc_start: 0.9002 (m-10) cc_final: 0.8672 (m-90) REVERT: I 73 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8499 (t) REVERT: I 76 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7615 (t80) REVERT: I 98 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7927 (mtm-85) REVERT: I 117 LYS cc_start: 0.9408 (mtmt) cc_final: 0.9189 (mtpp) REVERT: I 149 MET cc_start: 0.9166 (mmm) cc_final: 0.8951 (mmm) REVERT: I 191 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8737 (tt) REVERT: I 208 ASP cc_start: 0.8488 (t0) cc_final: 0.8179 (t70) REVERT: P 92 MET cc_start: 0.8858 (ttm) cc_final: 0.8577 (ttt) REVERT: P 283 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.6537 (ttm) REVERT: P 298 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6964 (t80) REVERT: P 328 MET cc_start: 0.7457 (mmm) cc_final: 0.7205 (mmm) REVERT: Q 78 ARG cc_start: 0.8553 (ptm-80) cc_final: 0.8190 (ptm-80) REVERT: Q 96 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8411 (mttp) REVERT: Q 126 LEU cc_start: 0.9090 (mt) cc_final: 0.8881 (mt) REVERT: R 45 ARG cc_start: 0.2504 (ptt180) cc_final: 0.1949 (tmm-80) REVERT: R 80 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8096 (t0) REVERT: S 40 ARG cc_start: 0.9137 (mtt180) cc_final: 0.8881 (mtm-85) REVERT: S 45 LYS cc_start: 0.9178 (tptt) cc_final: 0.8943 (mmmt) REVERT: S 62 GLN cc_start: 0.8889 (mp10) cc_final: 0.8587 (mp10) REVERT: T 129 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7404 (tp30) REVERT: V 53 ASN cc_start: 0.8962 (m-40) cc_final: 0.8517 (m-40) REVERT: W 24 PHE cc_start: 0.8783 (m-80) cc_final: 0.8402 (m-80) REVERT: W 54 GLN cc_start: 0.9099 (mt0) cc_final: 0.8553 (mp10) REVERT: W 61 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8643 (mm110) REVERT: W 91 MET cc_start: 0.8578 (mtt) cc_final: 0.8299 (mtt) REVERT: W 95 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8473 (mt-10) REVERT: W 109 PHE cc_start: 0.9033 (m-80) cc_final: 0.8818 (m-80) REVERT: X 32 TYR cc_start: 0.8701 (t80) cc_final: 0.8447 (t80) REVERT: a 53 ARG cc_start: 0.8503 (mtm110) cc_final: 0.7897 (ttt-90) REVERT: b 15 LYS cc_start: 0.9085 (pttp) cc_final: 0.8800 (mmtm) REVERT: b 32 MET cc_start: 0.8438 (mmm) cc_final: 0.7817 (tpt) REVERT: b 43 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8068 (m) REVERT: b 51 TYR cc_start: 0.8105 (m-80) cc_final: 0.7264 (t80) REVERT: q 42 ASP cc_start: 0.5939 (t70) cc_final: 0.5520 (t70) REVERT: q 68 MET cc_start: 0.6513 (ppp) cc_final: 0.6263 (ppp) REVERT: q 77 VAL cc_start: 0.8353 (t) cc_final: 0.8141 (p) outliers start: 185 outliers final: 117 residues processed: 899 average time/residue: 0.1994 time to fit residues: 296.1207 Evaluate side-chains 883 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 747 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 377 GLU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain G residue 584 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 649 VAL Chi-restraints excluded: chain G residue 665 PHE Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 96 LYS Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 154 LYS Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 124 ASP Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 107 MET Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 17 HIS Chi-restraints excluded: chain q residue 31 ASN Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 82 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 403 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 352 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 151 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 ASN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 HIS q 31 ASN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.101701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081344 restraints weight = 102081.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.082208 restraints weight = 45091.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.083088 restraints weight = 32847.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083564 restraints weight = 26505.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.083666 restraints weight = 24826.938| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 34767 Z= 0.201 Angle : 1.042 82.870 47131 Z= 0.391 Chirality : 0.048 0.272 5134 Planarity : 0.005 0.132 5962 Dihedral : 8.963 122.754 4936 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 3.65 % Allowed : 26.47 % Favored : 69.88 % 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: -0.42 (0.13), residues: 4121 helix: 0.58 (0.12), residues: 1897 sheet: -1.04 (0.26), residues: 397 loop : -0.94 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 212 TYR 0.039 0.002 TYR H 142 PHE 0.025 0.002 PHE P 310 TRP 0.063 0.002 TRP b 26 HIS 0.014 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00466 (34726) covalent geometry : angle 0.77207 (47039) SS BOND : bond 0.00174 ( 4) SS BOND : angle 0.42229 ( 8) hydrogen bonds : bond 0.04428 ( 1411) hydrogen bonds : angle 5.21386 ( 4116) metal coordination : bond 0.02363 ( 37) metal coordination : angle 16.58869 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 824 time to evaluate : 1.027 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 53 MET cc_start: 0.8241 (mpp) cc_final: 0.7527 (tpp) REVERT: B 103 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7872 (tp30) REVERT: B 122 ARG cc_start: 0.8627 (pmt170) cc_final: 0.8260 (pmt-80) REVERT: B 124 SER cc_start: 0.9069 (m) cc_final: 0.8390 (p) REVERT: B 131 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8278 (ttt) REVERT: B 147 LYS cc_start: 0.8868 (mttt) cc_final: 0.8252 (ttpt) REVERT: B 157 TYR cc_start: 0.8531 (m-80) cc_final: 0.8256 (m-80) REVERT: C 207 VAL cc_start: 0.9619 (m) cc_final: 0.9406 (p) REVERT: D 80 MET cc_start: 0.7770 (mmp) cc_final: 0.6788 (ptm) REVERT: D 105 MET cc_start: 0.8009 (tpp) cc_final: 0.7684 (tpp) REVERT: D 107 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7458 (mmm160) REVERT: D 125 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8180 (mt-10) REVERT: D 197 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8307 (ptm) REVERT: D 205 GLU cc_start: 0.8147 (tp30) cc_final: 0.7695 (tp30) REVERT: D 296 SER cc_start: 0.9042 (m) cc_final: 0.8825 (t) REVERT: D 446 ASP cc_start: 0.8570 (m-30) cc_final: 0.8226 (m-30) REVERT: E 58 ASN cc_start: 0.9049 (m-40) cc_final: 0.8768 (m-40) REVERT: E 98 ASN cc_start: 0.9061 (m-40) cc_final: 0.8667 (m110) REVERT: E 105 GLN cc_start: 0.9036 (pt0) cc_final: 0.8805 (pm20) REVERT: E 113 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7435 (mt-10) REVERT: E 145 ASP cc_start: 0.8968 (t0) cc_final: 0.8698 (t0) REVERT: E 181 ASN cc_start: 0.7898 (m-40) cc_final: 0.7600 (t0) REVERT: E 184 MET cc_start: 0.6546 (ptp) cc_final: 0.6321 (mtt) REVERT: E 186 GLN cc_start: 0.7940 (tp40) cc_final: 0.7624 (tp40) REVERT: F 413 TRP cc_start: 0.8394 (t60) cc_final: 0.8139 (t60) REVERT: F 448 ASP cc_start: 0.8260 (m-30) cc_final: 0.7860 (t0) REVERT: G 94 MET cc_start: 0.8775 (tpt) cc_final: 0.8501 (tpp) REVERT: G 97 MET cc_start: 0.6505 (mtm) cc_final: 0.6131 (mtm) REVERT: G 138 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8008 (t0) REVERT: G 264 SER cc_start: 0.9343 (m) cc_final: 0.8901 (p) REVERT: G 306 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8005 (mtm) REVERT: G 329 MET cc_start: 0.8311 (mtp) cc_final: 0.8094 (mtp) REVERT: G 396 GLU cc_start: 0.8254 (tt0) cc_final: 0.7877 (tp30) REVERT: G 605 GLN cc_start: 0.8078 (pp30) cc_final: 0.7730 (pp30) REVERT: G 608 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8634 (m) REVERT: G 618 GLU cc_start: 0.8772 (mp0) cc_final: 0.8390 (mp0) REVERT: G 707 MET cc_start: 0.9332 (mmm) cc_final: 0.9077 (mmm) REVERT: H 54 LYS cc_start: 0.9279 (ptmm) cc_final: 0.8608 (ptmt) REVERT: H 214 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6157 (tp30) REVERT: H 224 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7739 (t80) REVERT: H 247 TYR cc_start: 0.8067 (t80) cc_final: 0.7677 (t80) REVERT: H 282 TYR cc_start: 0.7870 (t80) cc_final: 0.7188 (t80) REVERT: H 286 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8308 (mpp) REVERT: H 292 ASN cc_start: 0.8319 (m-40) cc_final: 0.8095 (m-40) REVERT: I 63 TRP cc_start: 0.8910 (m-10) cc_final: 0.8679 (m-90) REVERT: I 73 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8388 (t) REVERT: I 76 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7816 (t80) REVERT: I 98 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7564 (mtm-85) REVERT: I 117 LYS cc_start: 0.9312 (mtmt) cc_final: 0.9072 (mtpp) REVERT: I 191 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8699 (tt) REVERT: I 208 ASP cc_start: 0.8415 (t0) cc_final: 0.8111 (t70) REVERT: P 79 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8501 (mt0) REVERT: P 92 MET cc_start: 0.8927 (ttm) cc_final: 0.8679 (ttt) REVERT: P 210 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7269 (tp30) REVERT: P 283 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.6890 (tpp) REVERT: P 288 PHE cc_start: 0.3545 (t80) cc_final: 0.3160 (t80) REVERT: P 298 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7097 (t80) REVERT: P 328 MET cc_start: 0.7445 (mmm) cc_final: 0.7182 (mmm) REVERT: Q 78 ARG cc_start: 0.8587 (ptm-80) cc_final: 0.8232 (ptm-80) REVERT: Q 96 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8400 (mttp) REVERT: Q 128 PHE cc_start: 0.8892 (m-80) cc_final: 0.8465 (m-10) REVERT: R 45 ARG cc_start: 0.2677 (ptt180) cc_final: 0.2176 (tmm-80) REVERT: R 80 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7865 (t0) REVERT: S 40 ARG cc_start: 0.9118 (mtt180) cc_final: 0.8730 (mtm-85) REVERT: S 45 LYS cc_start: 0.9142 (tptt) cc_final: 0.8906 (mmmt) REVERT: S 62 GLN cc_start: 0.8775 (mp10) cc_final: 0.8512 (mp10) REVERT: T 117 GLU cc_start: 0.8134 (pp20) cc_final: 0.7877 (pp20) REVERT: T 129 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7500 (tp30) REVERT: V 53 ASN cc_start: 0.8847 (m-40) cc_final: 0.8429 (m-40) REVERT: W 24 PHE cc_start: 0.8736 (m-80) cc_final: 0.8413 (m-80) REVERT: W 45 GLU cc_start: 0.8634 (tp30) cc_final: 0.7941 (tp30) REVERT: W 54 GLN cc_start: 0.9108 (mt0) cc_final: 0.8472 (mp10) REVERT: W 61 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8394 (mm110) REVERT: W 64 ASP cc_start: 0.8882 (m-30) cc_final: 0.8644 (p0) REVERT: W 91 MET cc_start: 0.8506 (mtt) cc_final: 0.8196 (mtt) REVERT: W 93 LEU cc_start: 0.9323 (tt) cc_final: 0.8981 (tt) REVERT: W 95 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8409 (mt-10) REVERT: X 32 TYR cc_start: 0.8728 (t80) cc_final: 0.8509 (t80) REVERT: Z 51 MET cc_start: 0.8507 (tmm) cc_final: 0.8304 (tmm) REVERT: a 15 CYS cc_start: 0.8560 (m) cc_final: 0.8352 (m) REVERT: a 48 MET cc_start: 0.8323 (mmm) cc_final: 0.8032 (mmm) REVERT: a 53 ARG cc_start: 0.8489 (mtm110) cc_final: 0.7865 (ttt-90) REVERT: a 60 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8161 (p90) REVERT: b 8 PHE cc_start: 0.7250 (t80) cc_final: 0.7012 (t80) REVERT: b 15 LYS cc_start: 0.9038 (pttp) cc_final: 0.8766 (mmtm) REVERT: b 32 MET cc_start: 0.8414 (mmm) cc_final: 0.7887 (tpt) REVERT: b 43 SER cc_start: 0.8515 (p) cc_final: 0.8114 (m) REVERT: b 51 TYR cc_start: 0.8023 (m-80) cc_final: 0.7331 (t80) REVERT: q 77 VAL cc_start: 0.8275 (t) cc_final: 0.8060 (p) REVERT: r 27 ARG cc_start: 0.6589 (ptp90) cc_final: 0.6289 (ptt90) outliers start: 132 outliers final: 93 residues processed: 900 average time/residue: 0.2021 time to fit residues: 299.1667 Evaluate side-chains 885 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 776 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 234 GLN Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 543 LYS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 665 PHE Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 ASP Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 96 LYS Chi-restraints excluded: chain Q residue 154 LYS Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 124 ASP Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 107 MET Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 17 HIS Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 82 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 2 optimal weight: 0.0470 chunk 390 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 322 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 394 optimal weight: 0.1980 chunk 227 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 312 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 151 GLN C 159 HIS ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS E 132 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 ASN T 101 ASN X 77 HIS ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN q 31 ASN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.104169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083638 restraints weight = 101471.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.085143 restraints weight = 44142.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.086087 restraints weight = 29910.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085930 restraints weight = 25589.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.086029 restraints weight = 24905.039| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 34767 Z= 0.149 Angle : 0.993 80.539 47131 Z= 0.385 Chirality : 0.047 0.340 5134 Planarity : 0.005 0.130 5962 Dihedral : 8.694 119.548 4936 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.42 % Favored : 95.56 % Rotamer: Outliers : 2.65 % Allowed : 27.91 % Favored : 69.44 % 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: -0.36 (0.13), residues: 4121 helix: 0.61 (0.12), residues: 1891 sheet: -1.04 (0.26), residues: 388 loop : -0.89 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG q 34 TYR 0.028 0.002 TYR H 142 PHE 0.027 0.002 PHE A 92 TRP 0.055 0.002 TRP F 62 HIS 0.012 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00346 (34726) covalent geometry : angle 0.76621 (47039) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.52058 ( 8) hydrogen bonds : bond 0.04242 ( 1411) hydrogen bonds : angle 5.09489 ( 4116) metal coordination : bond 0.01441 ( 37) metal coordination : angle 14.99352 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 845 time to evaluate : 1.139 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 53 MET cc_start: 0.8297 (mpp) cc_final: 0.7667 (tpp) REVERT: B 122 ARG cc_start: 0.8478 (pmt170) cc_final: 0.8096 (pmt-80) REVERT: B 131 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8388 (ttt) REVERT: B 147 LYS cc_start: 0.8812 (mttt) cc_final: 0.8126 (ttpt) REVERT: B 157 TYR cc_start: 0.8466 (m-80) cc_final: 0.8139 (m-80) REVERT: B 176 SER cc_start: 0.9097 (m) cc_final: 0.8823 (t) REVERT: D 80 MET cc_start: 0.7657 (mmp) cc_final: 0.6652 (ptm) REVERT: D 125 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8150 (mt-10) REVERT: D 205 GLU cc_start: 0.8081 (tp30) cc_final: 0.7571 (tp30) REVERT: E 58 ASN cc_start: 0.9011 (m-40) cc_final: 0.8760 (m-40) REVERT: E 83 ASP cc_start: 0.9362 (t0) cc_final: 0.8777 (m-30) REVERT: E 98 ASN cc_start: 0.9030 (m-40) cc_final: 0.8616 (m110) REVERT: E 105 GLN cc_start: 0.8994 (pt0) cc_final: 0.8765 (pm20) REVERT: E 113 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7931 (mt-10) REVERT: E 145 ASP cc_start: 0.8997 (t0) cc_final: 0.8786 (t0) REVERT: E 181 ASN cc_start: 0.7755 (m-40) cc_final: 0.7400 (t0) REVERT: E 184 MET cc_start: 0.6412 (ptp) cc_final: 0.6149 (mtt) REVERT: F 119 GLU cc_start: 0.6746 (pm20) cc_final: 0.6530 (pm20) REVERT: F 217 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8245 (tm-30) REVERT: F 377 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7534 (tp30) REVERT: F 386 ARG cc_start: 0.9000 (ttm110) cc_final: 0.8631 (ttp-110) REVERT: F 413 TRP cc_start: 0.8300 (t60) cc_final: 0.8006 (t60) REVERT: F 418 GLN cc_start: 0.8301 (mm110) cc_final: 0.8093 (mm-40) REVERT: F 448 ASP cc_start: 0.8258 (m-30) cc_final: 0.7822 (t0) REVERT: G 42 MET cc_start: 0.9247 (mmm) cc_final: 0.8962 (mmm) REVERT: G 94 MET cc_start: 0.8727 (tpt) cc_final: 0.8461 (tpp) REVERT: G 97 MET cc_start: 0.6412 (mtm) cc_final: 0.6185 (mtm) REVERT: G 138 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7979 (t0) REVERT: G 264 SER cc_start: 0.9317 (m) cc_final: 0.8866 (p) REVERT: G 306 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7958 (ttm) REVERT: G 396 GLU cc_start: 0.8194 (tt0) cc_final: 0.7848 (tp30) REVERT: G 605 GLN cc_start: 0.8129 (pp30) cc_final: 0.7814 (pp30) REVERT: G 608 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8527 (m) REVERT: G 618 GLU cc_start: 0.8738 (mp0) cc_final: 0.8403 (mp0) REVERT: G 707 MET cc_start: 0.9309 (mmm) cc_final: 0.9062 (mmm) REVERT: H 54 LYS cc_start: 0.9218 (ptmm) cc_final: 0.8763 (ptmt) REVERT: H 181 MET cc_start: 0.8884 (mtt) cc_final: 0.8515 (mtt) REVERT: H 214 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6203 (tm-30) REVERT: H 224 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7713 (t80) REVERT: H 234 MET cc_start: 0.9035 (mmm) cc_final: 0.8773 (mmm) REVERT: H 247 TYR cc_start: 0.8070 (t80) cc_final: 0.7703 (t80) REVERT: H 282 TYR cc_start: 0.7774 (t80) cc_final: 0.6857 (t80) REVERT: H 286 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8600 (mpp) REVERT: I 76 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7723 (t80) REVERT: I 98 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7206 (mtm-85) REVERT: I 117 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8805 (mtpp) REVERT: I 191 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8689 (tt) REVERT: I 208 ASP cc_start: 0.8432 (t0) cc_final: 0.8161 (t70) REVERT: P 79 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8498 (mt0) REVERT: P 97 MET cc_start: 0.8247 (ptp) cc_final: 0.7701 (ptp) REVERT: P 210 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7352 (tp30) REVERT: P 283 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.6739 (tpp) REVERT: P 288 PHE cc_start: 0.3334 (t80) cc_final: 0.3036 (t80) REVERT: P 298 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7047 (t80) REVERT: P 328 MET cc_start: 0.7503 (mmm) cc_final: 0.7259 (mmm) REVERT: Q 96 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8322 (mttp) REVERT: Q 128 PHE cc_start: 0.8617 (m-80) cc_final: 0.8404 (m-10) REVERT: Q 145 TYR cc_start: 0.8647 (p90) cc_final: 0.8193 (p90) REVERT: Q 156 LYS cc_start: 0.7499 (tptp) cc_final: 0.6679 (mmmm) REVERT: Q 165 SER cc_start: 0.8595 (m) cc_final: 0.8326 (p) REVERT: R 45 ARG cc_start: 0.2544 (ptt180) cc_final: 0.2085 (tmm-80) REVERT: S 40 ARG cc_start: 0.9151 (mtt180) cc_final: 0.8660 (mtm180) REVERT: S 45 LYS cc_start: 0.9144 (tptt) cc_final: 0.8919 (mmmt) REVERT: S 62 GLN cc_start: 0.8853 (mp10) cc_final: 0.8615 (mp10) REVERT: T 77 ASP cc_start: 0.8094 (t0) cc_final: 0.7324 (t0) REVERT: T 81 ASP cc_start: 0.9180 (t0) cc_final: 0.8969 (m-30) REVERT: T 82 ARG cc_start: 0.8389 (mmm160) cc_final: 0.8120 (mtp180) REVERT: T 117 GLU cc_start: 0.8322 (pp20) cc_final: 0.8007 (pp20) REVERT: V 53 ASN cc_start: 0.8835 (m-40) cc_final: 0.8401 (m-40) REVERT: W 45 GLU cc_start: 0.8645 (tp30) cc_final: 0.8098 (tp30) REVERT: W 53 MET cc_start: 0.8876 (mtt) cc_final: 0.8444 (mtt) REVERT: W 54 GLN cc_start: 0.9047 (mt0) cc_final: 0.8469 (mp10) REVERT: W 61 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8389 (mm110) REVERT: W 64 ASP cc_start: 0.8902 (m-30) cc_final: 0.8620 (p0) REVERT: W 91 MET cc_start: 0.8505 (mtt) cc_final: 0.8141 (mtt) REVERT: W 95 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8352 (mt-10) REVERT: X 32 TYR cc_start: 0.8793 (t80) cc_final: 0.8555 (t80) REVERT: X 111 VAL cc_start: 0.8677 (p) cc_final: 0.8467 (m) REVERT: a 40 ARG cc_start: 0.8209 (ptm160) cc_final: 0.7947 (ptm160) REVERT: a 53 ARG cc_start: 0.8479 (mtm110) cc_final: 0.7870 (ttt-90) REVERT: b 15 LYS cc_start: 0.9038 (pttp) cc_final: 0.8696 (mmtm) REVERT: b 32 MET cc_start: 0.8440 (mmm) cc_final: 0.7954 (tpt) REVERT: b 43 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8078 (m) REVERT: b 51 TYR cc_start: 0.7948 (m-80) cc_final: 0.7280 (t80) REVERT: q 42 ASP cc_start: 0.5944 (t70) cc_final: 0.5630 (t70) REVERT: r 27 ARG cc_start: 0.6480 (ptp90) cc_final: 0.6160 (ptt90) outliers start: 96 outliers final: 72 residues processed: 904 average time/residue: 0.2018 time to fit residues: 300.0938 Evaluate side-chains 885 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 799 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 377 GLU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 140 GLN Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 543 LYS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 665 PHE Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 64 PHE Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 96 LYS Chi-restraints excluded: chain Q residue 154 LYS Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 124 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 17 HIS Chi-restraints excluded: chain q residue 31 ASN Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 131 optimal weight: 7.9990 chunk 288 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 148 optimal weight: 0.6980 chunk 264 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 404 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 129 HIS ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.103354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082679 restraints weight = 102102.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084104 restraints weight = 44614.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.085082 restraints weight = 30955.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.084935 restraints weight = 26666.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.085063 restraints weight = 25780.915| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.7391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 34767 Z= 0.239 Angle : 1.158 80.515 47131 Z= 0.539 Chirality : 0.050 0.848 5134 Planarity : 0.006 0.155 5962 Dihedral : 8.698 119.551 4936 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 2.63 % Allowed : 28.35 % Favored : 69.02 % Cbeta Deviations : 0.05 % 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: -0.37 (0.13), residues: 4121 helix: 0.59 (0.12), residues: 1892 sheet: -0.99 (0.26), residues: 393 loop : -0.88 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG X 135 TYR 0.041 0.002 TYR b 53 PHE 0.027 0.002 PHE b 8 TRP 0.048 0.002 TRP F 62 HIS 0.055 0.002 HIS W 105 Details of bonding type rmsd covalent geometry : bond 0.00543 (34726) covalent geometry : angle 0.97137 (47039) SS BOND : bond 0.00945 ( 4) SS BOND : angle 0.57215 ( 8) hydrogen bonds : bond 0.04303 ( 1411) hydrogen bonds : angle 5.12639 ( 4116) metal coordination : bond 0.01534 ( 37) metal coordination : angle 14.97607 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8242 Ramachandran restraints generated. 4121 Oldfield, 0 Emsley, 4121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 803 time to evaluate : 1.293 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 53 MET cc_start: 0.8299 (mpp) cc_final: 0.7675 (tpp) REVERT: B 122 ARG cc_start: 0.8457 (pmt170) cc_final: 0.8096 (pmt-80) REVERT: B 131 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8347 (ttt) REVERT: B 147 LYS cc_start: 0.8821 (mttt) cc_final: 0.8142 (ttpt) REVERT: B 157 TYR cc_start: 0.8449 (m-80) cc_final: 0.8140 (m-80) REVERT: B 176 SER cc_start: 0.9154 (m) cc_final: 0.8825 (t) REVERT: D 80 MET cc_start: 0.7684 (mmp) cc_final: 0.6697 (ptt) REVERT: D 125 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8157 (mt-10) REVERT: D 205 GLU cc_start: 0.8075 (tp30) cc_final: 0.7568 (tp30) REVERT: E 58 ASN cc_start: 0.9033 (m-40) cc_final: 0.8764 (m-40) REVERT: E 83 ASP cc_start: 0.9366 (t0) cc_final: 0.8777 (m-30) REVERT: E 98 ASN cc_start: 0.9028 (m-40) cc_final: 0.8611 (m110) REVERT: E 105 GLN cc_start: 0.9007 (pt0) cc_final: 0.8772 (pm20) REVERT: E 113 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7929 (mt-10) REVERT: E 132 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7354 (mp10) REVERT: E 145 ASP cc_start: 0.9004 (t0) cc_final: 0.8797 (t0) REVERT: E 181 ASN cc_start: 0.7751 (m-40) cc_final: 0.7393 (t0) REVERT: E 184 MET cc_start: 0.6397 (ptp) cc_final: 0.6111 (mtt) REVERT: F 119 GLU cc_start: 0.6763 (pm20) cc_final: 0.6555 (pm20) REVERT: F 217 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8241 (tm-30) REVERT: F 377 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7536 (tp30) REVERT: F 386 ARG cc_start: 0.9006 (ttm110) cc_final: 0.8635 (ttp-110) REVERT: F 413 TRP cc_start: 0.8303 (t60) cc_final: 0.8004 (t60) REVERT: F 418 GLN cc_start: 0.8295 (mm110) cc_final: 0.8095 (mm-40) REVERT: F 448 ASP cc_start: 0.8276 (m-30) cc_final: 0.7836 (t0) REVERT: G 42 MET cc_start: 0.9258 (mmm) cc_final: 0.8980 (mmm) REVERT: G 94 MET cc_start: 0.8739 (tpt) cc_final: 0.8469 (tpp) REVERT: G 97 MET cc_start: 0.6463 (mtm) cc_final: 0.6217 (mtm) REVERT: G 138 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7923 (t0) REVERT: G 264 SER cc_start: 0.9319 (m) cc_final: 0.8869 (p) REVERT: G 306 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7961 (ttm) REVERT: G 396 GLU cc_start: 0.8203 (tt0) cc_final: 0.7857 (tp30) REVERT: G 605 GLN cc_start: 0.8098 (pp30) cc_final: 0.7808 (pp30) REVERT: G 608 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8536 (m) REVERT: G 618 GLU cc_start: 0.8735 (mp0) cc_final: 0.8396 (mp0) REVERT: G 707 MET cc_start: 0.9292 (mmm) cc_final: 0.9041 (mmm) REVERT: H 54 LYS cc_start: 0.9229 (ptmm) cc_final: 0.8762 (ptmt) REVERT: H 181 MET cc_start: 0.8881 (mtt) cc_final: 0.8506 (mtt) REVERT: H 214 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6199 (tm-30) REVERT: H 224 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7727 (t80) REVERT: H 234 MET cc_start: 0.9046 (mmm) cc_final: 0.8758 (mmm) REVERT: H 247 TYR cc_start: 0.8092 (t80) cc_final: 0.7744 (t80) REVERT: H 282 TYR cc_start: 0.7373 (t80) cc_final: 0.7034 (t80) REVERT: H 286 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8571 (mpp) REVERT: I 76 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7725 (t80) REVERT: I 98 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7220 (mtm-85) REVERT: I 117 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8807 (mtpp) REVERT: I 191 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8691 (tt) REVERT: I 208 ASP cc_start: 0.8441 (t0) cc_final: 0.8176 (t70) REVERT: P 79 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8486 (mt0) REVERT: P 97 MET cc_start: 0.8224 (ptp) cc_final: 0.7710 (ptp) REVERT: P 210 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7417 (tp30) REVERT: P 283 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.6739 (tpp) REVERT: P 288 PHE cc_start: 0.3315 (t80) cc_final: 0.3018 (t80) REVERT: P 298 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.7054 (t80) REVERT: P 328 MET cc_start: 0.7498 (mmm) cc_final: 0.7258 (mmm) REVERT: Q 96 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8327 (mttp) REVERT: Q 128 PHE cc_start: 0.8612 (m-80) cc_final: 0.8375 (m-10) REVERT: Q 145 TYR cc_start: 0.8653 (p90) cc_final: 0.8193 (p90) REVERT: Q 156 LYS cc_start: 0.7505 (tptp) cc_final: 0.6683 (mmmm) REVERT: Q 165 SER cc_start: 0.8584 (m) cc_final: 0.8338 (p) REVERT: R 45 ARG cc_start: 0.2445 (ptt180) cc_final: 0.2029 (tmm-80) REVERT: S 40 ARG cc_start: 0.9154 (mtt180) cc_final: 0.8658 (mtm180) REVERT: S 45 LYS cc_start: 0.9145 (tptt) cc_final: 0.8917 (mmmt) REVERT: S 62 GLN cc_start: 0.8854 (mp10) cc_final: 0.8616 (mp10) REVERT: T 77 ASP cc_start: 0.8130 (t0) cc_final: 0.7346 (t0) REVERT: T 81 ASP cc_start: 0.9250 (t0) cc_final: 0.9025 (m-30) REVERT: T 82 ARG cc_start: 0.8417 (mmm160) cc_final: 0.8118 (mtp180) REVERT: T 117 GLU cc_start: 0.8292 (pp20) cc_final: 0.8018 (pp20) REVERT: V 53 ASN cc_start: 0.8847 (m-40) cc_final: 0.8410 (m-40) REVERT: W 45 GLU cc_start: 0.8646 (tp30) cc_final: 0.8107 (tp30) REVERT: W 53 MET cc_start: 0.8890 (mtt) cc_final: 0.8462 (mtt) REVERT: W 54 GLN cc_start: 0.9057 (mt0) cc_final: 0.8474 (mp10) REVERT: W 61 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8391 (mm110) REVERT: W 64 ASP cc_start: 0.8919 (m-30) cc_final: 0.8633 (p0) REVERT: W 91 MET cc_start: 0.8505 (mtt) cc_final: 0.8170 (mtt) REVERT: W 95 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8372 (mt-10) REVERT: W 127 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8116 (ppp) REVERT: X 32 TYR cc_start: 0.8777 (t80) cc_final: 0.8538 (t80) REVERT: X 44 MET cc_start: 0.9061 (mtp) cc_final: 0.8837 (mtp) REVERT: X 111 VAL cc_start: 0.8676 (p) cc_final: 0.8468 (m) REVERT: a 40 ARG cc_start: 0.8168 (ptm160) cc_final: 0.7907 (ptm160) REVERT: a 53 ARG cc_start: 0.8484 (mtm110) cc_final: 0.7872 (ttt-90) REVERT: a 60 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8109 (p90) REVERT: b 15 LYS cc_start: 0.8955 (pttp) cc_final: 0.8707 (mmtm) REVERT: b 32 MET cc_start: 0.8450 (mmm) cc_final: 0.7976 (tpt) REVERT: b 43 SER cc_start: 0.8484 (p) cc_final: 0.8080 (m) REVERT: b 51 TYR cc_start: 0.7939 (m-80) cc_final: 0.7294 (t80) REVERT: q 31 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7315 (m110) REVERT: q 42 ASP cc_start: 0.5931 (t70) cc_final: 0.5622 (t70) REVERT: r 27 ARG cc_start: 0.6479 (ptp90) cc_final: 0.6152 (ptt90) outliers start: 95 outliers final: 78 residues processed: 859 average time/residue: 0.1975 time to fit residues: 280.5152 Evaluate side-chains 882 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 788 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 377 GLU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 543 LYS Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 665 PHE Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 64 PHE Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 96 LYS Chi-restraints excluded: chain Q residue 154 LYS Chi-restraints excluded: chain Q residue 166 TRP Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 HIS Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 124 ASP Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 17 HIS Chi-restraints excluded: chain q residue 31 ASN Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 231 optimal weight: 2.9990 chunk 345 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 316 optimal weight: 2.9990 chunk 95 optimal weight: 40.0000 chunk 142 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.103321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082687 restraints weight = 101427.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.083784 restraints weight = 44257.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.084657 restraints weight = 30960.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.085105 restraints weight = 26616.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.085071 restraints weight = 25534.050| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.7395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 34767 Z= 0.239 Angle : 1.158 80.515 47131 Z= 0.539 Chirality : 0.050 0.848 5134 Planarity : 0.006 0.155 5962 Dihedral : 8.698 119.551 4936 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 2.60 % Allowed : 28.60 % Favored : 68.80 % Cbeta Deviations : 0.05 % 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: -0.37 (0.13), residues: 4121 helix: 0.59 (0.12), residues: 1892 sheet: -0.99 (0.26), residues: 393 loop : -0.88 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG X 135 TYR 0.041 0.002 TYR b 53 PHE 0.027 0.002 PHE b 8 TRP 0.048 0.002 TRP F 62 HIS 0.055 0.002 HIS W 105 Details of bonding type rmsd covalent geometry : bond 0.00543 (34726) covalent geometry : angle 0.97137 (47039) SS BOND : bond 0.00945 ( 4) SS BOND : angle 0.57215 ( 8) hydrogen bonds : bond 0.04303 ( 1411) hydrogen bonds : angle 5.12639 ( 4116) metal coordination : bond 0.01534 ( 37) metal coordination : angle 14.97607 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7309.04 seconds wall clock time: 126 minutes 47.98 seconds (7607.98 seconds total)