Starting phenix.real_space_refine on Mon Jul 6 06:30:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnq_38511/07_2026/8xnq_38511_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnq_38511/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnq_38511/07_2026/8xnq_38511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnq_38511/07_2026/8xnq_38511.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnq_38511/07_2026/8xnq_38511_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnq_38511/07_2026/8xnq_38511_neut.cif" } 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.96, per 1000 atoms: 0.21 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: 3.31 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: 1.17 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: 7.23 Time building geometry restraints manager: 4.24 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=" 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 bond pdb=" C15 EHZ W 201 " pdb=" O4 EHZ W 201 " ideal model delta sigma weight residual 1.356 1.181 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" O7 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 1.486 1.642 -0.156 2.00e-02 2.50e+03 6.09e+01 ... (remaining 34721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.66: 46259 6.66 - 13.33: 613 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: 20233 27.43 - 54.87: 663 54.87 - 82.30: 88 82.30 - 109.74: 9 109.74 - 137.17: 3 Dihedral angle restraints: 20996 sinusoidal: 8882 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 20993 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: 4.590 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.750 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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= 1.048 Angle : 2.281 52.571 47131 Z= 1.521 Chirality : 0.133 0.915 5134 Planarity : 0.009 0.258 5962 Dihedral : 13.412 137.171 13174 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/Z covalent geometry : bond 0.01469 / 0.94 (34726) covalent geometry : angle 2.15512 / 1.52 (47039) SS BOND : bond 0.03600 / 1.82 ( 4) SS BOND : angle 5.78390 / 2.52 ( 8) hydrogen bonds : bond 0.24403 / 16.61 ( 1411) hydrogen bonds : angle 8.85727 / 6.33 ( 4116) metal coordination : bond 0.52816 / 33.81 ( 37) metal coordination : angle 17.72237 / 13.71 ( 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 : 1.116 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: 0.2454 time to fit residues: 640.5822 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 : 1.383 ------------------------------------------------------------------------------- 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... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.110062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087387 restraints weight = 102319.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090527 restraints weight = 48490.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092581 restraints weight = 27276.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092448 restraints weight = 22050.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092553 restraints weight = 20392.401| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 34767 Z= 0.210 Angle : 1.052 70.156 47131 Z= 0.451 Chirality : 0.050 0.202 5134 Planarity : 0.007 0.120 5962 Dihedral : 9.552 150.261 4956 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 3.95 % Allowed : 18.07 % Favored : 77.98 % 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: -0.97 (0.13), residues: 4121 helix: 0.17 (0.11), residues: 1890 sheet: -0.96 (0.27), residues: 360 loop : -1.38 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 81 TYR 0.029 0.003 TYR B 112 PHE 0.024 0.003 PHE H 310 TRP 0.045 0.003 TRP D 300 HIS 0.012 0.002 HIS P 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (34726) covalent geometry : angle 0.87527 / 0.45 (47039) SS BOND : bond 0.00177 / 0.09 ( 4) SS BOND : angle 1.63295 / 0.74 ( 8) hydrogen bonds : bond 0.05965 / 3.99 ( 1411) hydrogen bonds : angle 5.74648 / 4.11 ( 4116) metal coordination : bond 0.02582 / 1.47 ( 37) metal coordination : angle 13.85828 / 10.28 ( 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 1267 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1124 time to evaluate : 1.334 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: A 1 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5363 (tpp) REVERT: A 18 ILE cc_start: 0.9261 (mm) cc_final: 0.8984 (mm) REVERT: A 24 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8867 (tp) REVERT: A 54 LYS cc_start: 0.8364 (ptmt) cc_final: 0.8093 (ptmt) REVERT: A 83 LYS cc_start: 0.6383 (mttt) cc_final: 0.6167 (mmtt) REVERT: A 104 TYR cc_start: 0.8581 (t80) cc_final: 0.8314 (t80) REVERT: B 112 TYR cc_start: 0.7243 (m-80) cc_final: 0.7008 (m-80) REVERT: B 121 PHE cc_start: 0.8727 (t80) cc_final: 0.8517 (t80) REVERT: B 122 ARG cc_start: 0.8943 (pmt170) cc_final: 0.8439 (pmt-80) REVERT: B 147 LYS cc_start: 0.8964 (mttt) cc_final: 0.8618 (ttpt) REVERT: B 157 TYR cc_start: 0.8305 (m-80) cc_final: 0.8063 (m-80) REVERT: B 215 GLU cc_start: 0.7715 (tp30) cc_final: 0.7508 (tp30) REVERT: C 74 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7604 (tm-30) REVERT: C 93 ILE cc_start: 0.8852 (mm) cc_final: 0.8548 (mt) REVERT: C 153 ASP cc_start: 0.8372 (t0) cc_final: 0.8159 (t0) REVERT: C 172 MET cc_start: 0.8566 (mmm) cc_final: 0.8358 (mmm) REVERT: C 221 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7526 (mt-10) REVERT: D 156 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7627 (mt-10) REVERT: D 185 MET cc_start: 0.8909 (tpp) cc_final: 0.8478 (tpt) REVERT: D 292 MET cc_start: 0.8493 (tpp) cc_final: 0.8203 (mmt) REVERT: D 443 MET cc_start: 0.8651 (mpp) cc_final: 0.8418 (mpp) REVERT: E 58 ASN cc_start: 0.8696 (m-40) cc_final: 0.8447 (m-40) REVERT: E 98 ASN cc_start: 0.8819 (m-40) cc_final: 0.7978 (m110) REVERT: E 105 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: E 113 GLU cc_start: 0.7707 (mt-10) cc_final: 0.6944 (mt-10) REVERT: E 118 TYR cc_start: 0.8431 (m-80) cc_final: 0.8042 (m-80) REVERT: E 184 MET cc_start: 0.7800 (ttm) cc_final: 0.7597 (ptp) REVERT: E 194 ASP cc_start: 0.7039 (t0) cc_final: 0.6322 (p0) REVERT: F 77 LEU cc_start: 0.9086 (tt) cc_final: 0.8824 (pp) REVERT: F 124 THR cc_start: 0.8276 (m) cc_final: 0.7946 (p) REVERT: F 155 TYR cc_start: 0.8494 (m-80) cc_final: 0.7975 (m-80) REVERT: F 168 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8141 (t0) REVERT: F 337 MET cc_start: 0.8009 (mmm) cc_final: 0.7219 (mmp) REVERT: F 390 ASP cc_start: 0.7465 (t0) cc_final: 0.6663 (t70) REVERT: F 413 TRP cc_start: 0.8168 (t60) cc_final: 0.7938 (t60) REVERT: G 77 MET cc_start: 0.8337 (tpp) cc_final: 0.8096 (tpp) REVERT: G 100 TRP cc_start: 0.6343 (m100) cc_final: 0.6133 (m100) REVERT: G 138 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7635 (t0) REVERT: G 264 SER cc_start: 0.9303 (m) cc_final: 0.8679 (p) REVERT: G 283 GLU cc_start: 0.7926 (pm20) cc_final: 0.7518 (pt0) REVERT: G 347 ASP cc_start: 0.8392 (p0) cc_final: 0.7699 (p0) REVERT: G 427 LEU cc_start: 0.8892 (mt) cc_final: 0.8649 (mt) REVERT: G 459 ARG cc_start: 0.7177 (mtm180) cc_final: 0.6755 (ptm-80) REVERT: G 707 MET cc_start: 0.9293 (mmm) cc_final: 0.9053 (mmm) REVERT: H 43 TYR cc_start: 0.8690 (m-80) cc_final: 0.8044 (m-10) REVERT: H 134 ARG cc_start: 0.8613 (ptm160) cc_final: 0.8292 (ptm160) REVERT: H 172 MET cc_start: 0.7358 (ppp) cc_final: 0.6841 (ppp) REVERT: H 181 MET cc_start: 0.8590 (mtt) cc_final: 0.7957 (mtt) REVERT: H 224 PHE cc_start: 0.8456 (t80) cc_final: 0.7928 (t80) REVERT: H 268 SER cc_start: 0.9407 (m) cc_final: 0.9042 (t) REVERT: H 282 TYR cc_start: 0.7698 (t80) cc_final: 0.7084 (t80) REVERT: H 286 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8058 (mpp) REVERT: I 42 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6373 (tptt) REVERT: I 55 ASP cc_start: 0.8313 (m-30) cc_final: 0.8046 (t70) REVERT: I 63 TRP cc_start: 0.8700 (m-10) cc_final: 0.8391 (m-90) REVERT: I 149 MET cc_start: 0.9268 (mmm) cc_final: 0.8957 (mmm) REVERT: I 208 ASP cc_start: 0.8065 (t0) cc_final: 0.7767 (t70) REVERT: P 169 HIS cc_start: 0.6966 (t-90) cc_final: 0.6673 (t-170) REVERT: P 174 MET cc_start: 0.6960 (tpp) cc_final: 0.6493 (tmm) REVERT: P 181 LEU cc_start: 0.8211 (mp) cc_final: 0.7796 (mm) REVERT: P 271 TYR cc_start: 0.7238 (m-80) cc_final: 0.6385 (m-80) REVERT: P 328 MET cc_start: 0.7692 (tpp) cc_final: 0.7360 (mmm) REVERT: Q 128 PHE cc_start: 0.8368 (m-80) cc_final: 0.7710 (m-10) REVERT: R 61 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.5254 (mp) REVERT: R 106 TYR cc_start: 0.8873 (m-80) cc_final: 0.7870 (m-80) REVERT: S 40 ARG cc_start: 0.8772 (mtt180) cc_final: 0.8535 (mtm-85) REVERT: T 108 LEU cc_start: 0.8040 (mt) cc_final: 0.7344 (mt) REVERT: T 120 MET cc_start: 0.9063 (tpp) cc_final: 0.8536 (tpp) REVERT: W 36 ARG cc_start: 0.9193 (mtt90) cc_final: 0.8726 (mtt90) REVERT: W 45 GLU cc_start: 0.8457 (tp30) cc_final: 0.8233 (tm-30) REVERT: W 49 THR cc_start: 0.9569 (p) cc_final: 0.8925 (p) REVERT: W 69 MET cc_start: 0.8422 (mmt) cc_final: 0.8204 (mmt) REVERT: W 73 ASN cc_start: 0.8819 (m-40) cc_final: 0.8587 (m110) REVERT: W 110 PHE cc_start: 0.8110 (m-80) cc_final: 0.7633 (m-80) REVERT: X 82 PHE cc_start: 0.8412 (t80) cc_final: 0.8106 (t80) REVERT: X 91 TYR cc_start: 0.7318 (t80) cc_final: 0.6528 (t80) REVERT: Z 65 LEU cc_start: 0.9091 (mt) cc_final: 0.8800 (mt) REVERT: a 53 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8000 (ttt-90) REVERT: b 32 MET cc_start: 0.8969 (mmp) cc_final: 0.8660 (mmm) REVERT: b 43 SER cc_start: 0.8103 (t) cc_final: 0.7517 (m) REVERT: b 44 MET cc_start: 0.8333 (mtp) cc_final: 0.7316 (ptp) REVERT: b 51 TYR cc_start: 0.7947 (m-80) cc_final: 0.6902 (t80) REVERT: q 35 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7009 (mm) REVERT: q 68 MET cc_start: 0.6413 (ppp) cc_final: 0.6100 (ppp) REVERT: q 142 THR cc_start: 0.7905 (m) cc_final: 0.7672 (p) REVERT: r 96 THR cc_start: 0.9213 (p) cc_final: 0.8824 (t) REVERT: r 101 MET cc_start: 0.8103 (ttp) cc_final: 0.7898 (ttm) REVERT: r 110 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7546 (pt0) outliers start: 143 outliers final: 59 residues processed: 1205 average time/residue: 0.2164 time to fit residues: 424.3775 Evaluate side-chains 948 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 880 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 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 E residue 123 ARG 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 357 MET 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 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 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 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: 9.9990 chunk 307 optimal weight: 10.0000 chunk 336 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 346 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 371 optimal weight: 4.9990 chunk 318 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** 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 140 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN G 571 HIS ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 215 ASN P 251 ASN ** Q 88 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 W 129 HIS X 73 GLN a 58 ASN b 52 ASN q 72 ASN r 110 GLN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.106366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.082552 restraints weight = 103187.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.085458 restraints weight = 48899.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.087289 restraints weight = 30802.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088403 restraints weight = 23176.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.089075 restraints weight = 19606.119| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34767 Z= 0.208 Angle : 0.976 74.315 47131 Z= 0.398 Chirality : 0.048 0.256 5134 Planarity : 0.006 0.125 5962 Dihedral : 9.307 170.344 4952 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 4.48 % Allowed : 20.34 % Favored : 75.19 % 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: 0.50 (0.12), residues: 1889 sheet: -0.99 (0.26), residues: 371 loop : -1.12 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 98 TYR 0.029 0.002 TYR B 170 PHE 0.034 0.002 PHE G 462 TRP 0.038 0.002 TRP a 45 HIS 0.022 0.002 HIS S 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (34726) covalent geometry : angle 0.77484 / 0.39 (47039) SS BOND : bond 0.00178 / 0.09 ( 4) SS BOND : angle 0.53615 / 0.30 ( 8) hydrogen bonds : bond 0.05050 / 3.35 ( 1411) hydrogen bonds : angle 5.37716 / 3.83 ( 4116) metal coordination : bond 0.02569 / 1.49 ( 37) metal coordination : angle 14.08985 / 10.45 ( 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 1103 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 941 time to evaluate : 1.362 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: A 54 LYS cc_start: 0.8645 (ptmt) cc_final: 0.8432 (ptmt) REVERT: A 72 LEU cc_start: 0.9412 (mt) cc_final: 0.9201 (mt) REVERT: A 79 ILE cc_start: 0.9150 (mm) cc_final: 0.8935 (mm) REVERT: B 77 LYS cc_start: 0.8976 (mttt) cc_final: 0.8735 (mttt) REVERT: B 112 TYR cc_start: 0.7203 (m-80) cc_final: 0.6919 (m-80) REVERT: B 122 ARG cc_start: 0.8901 (pmt170) cc_final: 0.8681 (pmt-80) REVERT: B 147 LYS cc_start: 0.8900 (mttt) cc_final: 0.8441 (ttpt) REVERT: B 157 TYR cc_start: 0.8419 (m-80) cc_final: 0.8128 (m-80) REVERT: C 53 THR cc_start: 0.9599 (m) cc_final: 0.9356 (p) REVERT: C 93 ILE cc_start: 0.8913 (mm) cc_final: 0.8600 (mt) REVERT: D 205 GLU cc_start: 0.8031 (tp30) cc_final: 0.7552 (tp30) REVERT: D 300 TRP cc_start: 0.8702 (t-100) cc_final: 0.8374 (t-100) REVERT: D 371 MET cc_start: 0.9102 (ptm) cc_final: 0.8751 (ttp) REVERT: D 375 MET cc_start: 0.7870 (tpp) cc_final: 0.7660 (tpp) REVERT: D 443 MET cc_start: 0.8737 (mpp) cc_final: 0.8365 (mpp) REVERT: D 461 ILE cc_start: 0.9431 (mp) cc_final: 0.9147 (mt) REVERT: E 58 ASN cc_start: 0.8652 (m-40) cc_final: 0.8088 (m-40) REVERT: E 88 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8735 (tt0) REVERT: E 105 GLN cc_start: 0.8929 (pt0) cc_final: 0.8262 (pm20) REVERT: E 113 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7079 (mt-10) REVERT: E 124 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8111 (ttpt) REVERT: E 143 ASP cc_start: 0.8256 (m-30) cc_final: 0.7882 (t0) REVERT: E 180 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7267 (p) REVERT: E 181 ASN cc_start: 0.7800 (m-40) cc_final: 0.7476 (t0) REVERT: E 191 TYR cc_start: 0.6043 (m-80) cc_final: 0.5381 (m-80) REVERT: F 77 LEU cc_start: 0.9074 (tt) cc_final: 0.8820 (pp) REVERT: F 124 THR cc_start: 0.8496 (m) cc_final: 0.8020 (p) REVERT: F 209 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8092 (mp0) REVERT: F 337 MET cc_start: 0.8003 (mmm) cc_final: 0.7211 (mmp) REVERT: F 387 GLU cc_start: 0.7923 (mp0) cc_final: 0.7706 (mp0) REVERT: F 413 TRP cc_start: 0.8233 (t60) cc_final: 0.7834 (t60) REVERT: G 77 MET cc_start: 0.8736 (tpp) cc_final: 0.8467 (tpp) REVERT: G 94 MET cc_start: 0.8705 (tpt) cc_final: 0.8157 (tpp) REVERT: G 138 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7867 (t0) REVERT: G 264 SER cc_start: 0.9254 (m) cc_final: 0.8821 (p) REVERT: G 282 ASN cc_start: 0.7706 (p0) cc_final: 0.7465 (p0) REVERT: G 396 GLU cc_start: 0.8186 (tt0) cc_final: 0.7832 (tp30) REVERT: G 544 MET cc_start: 0.7847 (tmm) cc_final: 0.7442 (tmt) REVERT: G 548 LEU cc_start: 0.9248 (tp) cc_final: 0.9026 (tp) REVERT: G 605 GLN cc_start: 0.7828 (pp30) cc_final: 0.7373 (pp30) REVERT: G 618 GLU cc_start: 0.8583 (mp0) cc_final: 0.8269 (mp0) REVERT: G 628 GLU cc_start: 0.8478 (tt0) cc_final: 0.8187 (tt0) REVERT: G 707 MET cc_start: 0.9347 (mmm) cc_final: 0.9131 (mmm) REVERT: H 15 ILE cc_start: 0.9184 (mm) cc_final: 0.8940 (mt) REVERT: H 43 TYR cc_start: 0.8808 (m-80) cc_final: 0.8138 (m-10) REVERT: H 96 ILE cc_start: 0.8787 (mm) cc_final: 0.8400 (mm) REVERT: H 134 ARG cc_start: 0.8570 (ptm160) cc_final: 0.7939 (ptm160) REVERT: H 155 LEU cc_start: 0.9429 (mt) cc_final: 0.9164 (tp) REVERT: H 172 MET cc_start: 0.7590 (ppp) cc_final: 0.7200 (ppp) REVERT: H 181 MET cc_start: 0.8833 (mtt) cc_final: 0.8283 (mtt) REVERT: H 200 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8370 (pp) REVERT: H 247 TYR cc_start: 0.8115 (t80) cc_final: 0.7864 (t80) REVERT: H 251 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8794 (pp) REVERT: H 268 SER cc_start: 0.9343 (m) cc_final: 0.9013 (t) REVERT: H 282 TYR cc_start: 0.7831 (t80) cc_final: 0.7265 (t80) REVERT: H 286 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8337 (mpp) REVERT: H 292 ASN cc_start: 0.8136 (m-40) cc_final: 0.7849 (m-40) REVERT: H 318 MET cc_start: 0.7149 (ttt) cc_final: 0.6418 (tmm) REVERT: I 42 LYS cc_start: 0.6854 (mmtt) cc_final: 0.6208 (tptt) REVERT: I 55 ASP cc_start: 0.8300 (m-30) cc_final: 0.7900 (t70) REVERT: I 63 TRP cc_start: 0.8879 (m-10) cc_final: 0.8651 (m-10) REVERT: I 117 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8980 (mtpp) REVERT: I 191 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8442 (tt) REVERT: I 208 ASP cc_start: 0.8168 (t0) cc_final: 0.7891 (t70) REVERT: P 283 MET cc_start: 0.7673 (mmp) cc_final: 0.5986 (tpp) REVERT: Q 78 ARG cc_start: 0.8581 (ptm-80) cc_final: 0.8334 (ptm-80) REVERT: Q 128 PHE cc_start: 0.8394 (m-80) cc_final: 0.7731 (m-80) REVERT: R 73 GLU cc_start: 0.8209 (pm20) cc_final: 0.7534 (mp0) REVERT: R 106 TYR cc_start: 0.9030 (m-80) cc_final: 0.8547 (m-80) REVERT: S 40 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8083 (mtm-85) REVERT: T 80 LYS cc_start: 0.8914 (mttt) cc_final: 0.8610 (mmtt) REVERT: T 118 ILE cc_start: 0.8797 (mm) cc_final: 0.8516 (mm) REVERT: T 119 ILE cc_start: 0.9337 (mm) cc_final: 0.9036 (mm) REVERT: W 24 PHE cc_start: 0.8331 (m-10) cc_final: 0.7913 (m-80) REVERT: W 30 GLU cc_start: 0.8722 (tt0) cc_final: 0.8511 (pt0) REVERT: W 69 MET cc_start: 0.8682 (mmt) cc_final: 0.8468 (mmt) REVERT: W 87 ILE cc_start: 0.9616 (mm) cc_final: 0.9310 (mm) REVERT: W 95 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8502 (mt-10) REVERT: X 52 ASP cc_start: 0.6503 (p0) cc_final: 0.6302 (p0) REVERT: Z 65 LEU cc_start: 0.9191 (mt) cc_final: 0.8902 (mt) REVERT: a 53 ARG cc_start: 0.8529 (mtm110) cc_final: 0.7996 (ttt-90) REVERT: b 15 LYS cc_start: 0.8953 (pttp) cc_final: 0.8602 (mmtm) REVERT: b 32 MET cc_start: 0.8989 (mmp) cc_final: 0.8740 (mmm) REVERT: b 51 TYR cc_start: 0.8345 (m-80) cc_final: 0.7065 (t80) REVERT: q 142 THR cc_start: 0.8098 (m) cc_final: 0.7756 (p) REVERT: q 144 TYR cc_start: 0.5766 (m-80) cc_final: 0.5556 (m-80) REVERT: r 104 TRP cc_start: 0.8775 (m-10) cc_final: 0.8515 (m-10) REVERT: s 87 LEU cc_start: 0.7167 (pp) cc_final: 0.6901 (pp) outliers start: 162 outliers final: 88 residues processed: 1035 average time/residue: 0.2026 time to fit residues: 344.6714 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 : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 66 GLU Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 183 LEU 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 59 TYR Chi-restraints excluded: chain E residue 88 GLN 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 F residue 294 VAL 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 138 ASP Chi-restraints excluded: chain G residue 169 VAL 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 543 LYS 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 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 116 ILE Chi-restraints excluded: chain H residue 138 GLN Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 251 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 71 ASN 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 345 LEU Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain Q residue 54 THR 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 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 64 LYS Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 93 ASN Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 87 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 X residue 69 ASN Chi-restraints excluded: chain X residue 135 ARG 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 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 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: 3.9990 chunk 389 optimal weight: 0.0870 chunk 157 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 308 optimal weight: 30.0000 chunk 366 optimal weight: 9.9990 chunk 191 optimal weight: 0.8980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 122 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** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 HIS ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Q 88 GLN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 HIS T 101 ASN W 73 ASN W 129 HIS ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 ASN b 69 HIS q 17 HIS q 31 ASN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.107654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085515 restraints weight = 101249.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088590 restraints weight = 49039.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.090658 restraints weight = 27115.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.090365 restraints weight = 21440.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.090637 restraints weight = 20629.095| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34767 Z= 0.151 Angle : 0.925 76.318 47131 Z= 0.368 Chirality : 0.046 0.283 5134 Planarity : 0.005 0.126 5962 Dihedral : 9.185 177.002 4952 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 3.79 % Allowed : 21.86 % Favored : 74.36 % 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: 0.59 (0.12), residues: 1891 sheet: -0.86 (0.26), residues: 387 loop : -1.01 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 89 TYR 0.025 0.002 TYR P 89 PHE 0.032 0.002 PHE X 82 TRP 0.043 0.002 TRP F 62 HIS 0.010 0.001 HIS b 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (34726) covalent geometry : angle 0.72763 / 0.36 (47039) SS BOND : bond 0.00235 / 0.12 ( 4) SS BOND : angle 0.45178 / 0.24 ( 8) hydrogen bonds : bond 0.04463 / 2.96 ( 1411) hydrogen bonds : angle 5.13621 / 3.66 ( 4116) metal coordination : bond 0.01561 / 0.96 ( 37) metal coordination : angle 13.56644 / 10.10 ( 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 1079 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 942 time to evaluate : 1.346 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: A 8 PHE cc_start: 0.8454 (m-10) cc_final: 0.8205 (t80) REVERT: A 53 MET cc_start: 0.8232 (mpp) cc_final: 0.7435 (tpp) REVERT: B 122 ARG cc_start: 0.8845 (pmt170) cc_final: 0.8319 (tpt-90) REVERT: B 147 LYS cc_start: 0.8837 (mttt) cc_final: 0.8381 (ttpt) REVERT: B 157 TYR cc_start: 0.8343 (m-80) cc_final: 0.7690 (m-80) REVERT: B 203 TYR cc_start: 0.9195 (t80) cc_final: 0.8989 (t80) REVERT: C 93 ILE cc_start: 0.8853 (mm) cc_final: 0.8636 (mt) REVERT: C 117 ASP cc_start: 0.8425 (t0) cc_final: 0.8150 (t0) REVERT: D 197 MET cc_start: 0.8517 (ptm) cc_final: 0.7252 (ptm) REVERT: D 201 PHE cc_start: 0.8461 (m-80) cc_final: 0.8211 (m-80) REVERT: D 205 GLU cc_start: 0.7991 (tp30) cc_final: 0.7600 (tp30) REVERT: D 300 TRP cc_start: 0.8666 (t-100) cc_final: 0.8006 (t-100) REVERT: D 375 MET cc_start: 0.7590 (tpp) cc_final: 0.7388 (tpp) REVERT: D 443 MET cc_start: 0.8729 (mpp) cc_final: 0.8309 (mpp) REVERT: D 461 ILE cc_start: 0.9343 (mp) cc_final: 0.9142 (mt) REVERT: E 105 GLN cc_start: 0.8887 (pt0) cc_final: 0.8373 (pm20) REVERT: E 113 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7084 (mt-10) REVERT: E 181 ASN cc_start: 0.7806 (m-40) cc_final: 0.7145 (t0) REVERT: E 184 MET cc_start: 0.7037 (ptm) cc_final: 0.6472 (ptp) REVERT: F 77 LEU cc_start: 0.9048 (tt) cc_final: 0.8836 (pp) REVERT: F 276 PHE cc_start: 0.6624 (m-80) cc_final: 0.6287 (m-10) REVERT: F 337 MET cc_start: 0.7968 (mmm) cc_final: 0.7190 (mmp) REVERT: G 77 MET cc_start: 0.8874 (tpp) cc_final: 0.8536 (tpp) REVERT: G 94 MET cc_start: 0.8708 (tpt) cc_final: 0.8187 (tpp) REVERT: G 117 MET cc_start: 0.8790 (tpp) cc_final: 0.8566 (mmt) REVERT: G 126 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8783 (pp) REVERT: G 136 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8225 (mt-10) REVERT: G 138 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7872 (t0) REVERT: G 264 SER cc_start: 0.9218 (m) cc_final: 0.8798 (p) REVERT: G 396 GLU cc_start: 0.8152 (tt0) cc_final: 0.7737 (tp30) REVERT: G 496 MET cc_start: 0.8993 (ppp) cc_final: 0.8746 (ppp) REVERT: G 605 GLN cc_start: 0.7902 (pp30) cc_final: 0.7499 (pp30) REVERT: G 608 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8537 (m) REVERT: G 618 GLU cc_start: 0.8660 (mp0) cc_final: 0.8306 (mp0) REVERT: G 628 GLU cc_start: 0.8559 (tt0) cc_final: 0.8357 (tt0) REVERT: G 707 MET cc_start: 0.9286 (mmm) cc_final: 0.9062 (mmm) REVERT: H 15 ILE cc_start: 0.9190 (mm) cc_final: 0.8957 (mt) REVERT: H 43 TYR cc_start: 0.8729 (m-80) cc_final: 0.8114 (m-10) REVERT: H 54 LYS cc_start: 0.9109 (ptmm) cc_final: 0.8818 (ptmm) REVERT: H 134 ARG cc_start: 0.8528 (ptm160) cc_final: 0.8147 (ptm160) REVERT: H 172 MET cc_start: 0.7687 (ppp) cc_final: 0.7291 (ppp) REVERT: H 173 TRP cc_start: 0.8025 (m-10) cc_final: 0.7476 (m-90) REVERT: H 181 MET cc_start: 0.8895 (mtt) cc_final: 0.8433 (mtt) REVERT: H 184 MET cc_start: 0.8696 (mmt) cc_final: 0.8297 (mmt) REVERT: H 234 MET cc_start: 0.9075 (mmm) cc_final: 0.8755 (mmm) REVERT: H 247 TYR cc_start: 0.8059 (t80) cc_final: 0.7742 (t80) REVERT: H 282 TYR cc_start: 0.7672 (t80) cc_final: 0.7207 (t80) REVERT: H 286 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8496 (mpp) REVERT: H 292 ASN cc_start: 0.8220 (m-40) cc_final: 0.7884 (m-40) REVERT: H 317 TYR cc_start: 0.8000 (t80) cc_final: 0.7764 (t80) REVERT: H 318 MET cc_start: 0.7115 (ttt) cc_final: 0.5960 (tmm) REVERT: I 55 ASP cc_start: 0.8257 (m-30) cc_final: 0.7834 (t70) REVERT: I 76 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7412 (t80) REVERT: I 94 SER cc_start: 0.8613 (p) cc_final: 0.8333 (p) REVERT: I 98 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7466 (mtm-85) REVERT: I 117 LYS cc_start: 0.9036 (mtmt) cc_final: 0.8784 (mtpp) REVERT: I 208 ASP cc_start: 0.8131 (t0) cc_final: 0.7626 (t70) REVERT: P 283 MET cc_start: 0.7627 (mmp) cc_final: 0.5840 (tpp) REVERT: Q 78 ARG cc_start: 0.8591 (ptm-80) cc_final: 0.8381 (ptm-80) REVERT: Q 99 MET cc_start: 0.9102 (ptp) cc_final: 0.8681 (ptp) REVERT: Q 128 PHE cc_start: 0.8274 (m-80) cc_final: 0.7850 (m-80) REVERT: Q 166 TRP cc_start: 0.7833 (OUTLIER) cc_final: 0.6624 (m100) REVERT: R 73 GLU cc_start: 0.8209 (pm20) cc_final: 0.7527 (mp0) REVERT: R 74 HIS cc_start: 0.7771 (t-90) cc_final: 0.7130 (t-170) REVERT: R 80 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7498 (t0) REVERT: R 106 TYR cc_start: 0.9069 (m-80) cc_final: 0.8655 (m-80) REVERT: S 40 ARG cc_start: 0.9075 (mtt180) cc_final: 0.8714 (mtm-85) REVERT: S 45 LYS cc_start: 0.9043 (tptt) cc_final: 0.8610 (mmmt) REVERT: S 57 GLU cc_start: 0.6495 (pm20) cc_final: 0.6275 (pm20) REVERT: S 64 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6322 (mtmm) REVERT: T 80 LYS cc_start: 0.8823 (mttt) cc_final: 0.8480 (mmtt) REVERT: T 118 ILE cc_start: 0.8790 (mm) cc_final: 0.8589 (mm) REVERT: T 138 LEU cc_start: 0.9199 (tp) cc_final: 0.8974 (tp) REVERT: V 97 TRP cc_start: 0.7769 (m-10) cc_final: 0.7522 (m-10) REVERT: W 42 TRP cc_start: 0.9358 (m100) cc_final: 0.8585 (m100) REVERT: W 45 GLU cc_start: 0.8477 (tp30) cc_final: 0.7914 (tp30) REVERT: W 61 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8529 (mm-40) REVERT: W 69 MET cc_start: 0.8678 (mmt) cc_final: 0.8469 (mmt) REVERT: W 83 ASP cc_start: 0.7847 (t0) cc_final: 0.7358 (t0) REVERT: W 91 MET cc_start: 0.8340 (mtp) cc_final: 0.8105 (mtt) REVERT: W 109 PHE cc_start: 0.8685 (m-80) cc_final: 0.8477 (m-80) REVERT: X 43 PHE cc_start: 0.7914 (t80) cc_final: 0.7615 (t80) REVERT: Z 65 LEU cc_start: 0.9185 (mt) cc_final: 0.8919 (mt) REVERT: Z 76 GLN cc_start: 0.8515 (tp40) cc_final: 0.7869 (tp-100) REVERT: a 40 ARG cc_start: 0.7810 (ptm-80) cc_final: 0.7083 (ptm160) REVERT: a 53 ARG cc_start: 0.8435 (mtm110) cc_final: 0.7925 (ttt-90) REVERT: a 59 ARG cc_start: 0.7551 (ptt90) cc_final: 0.7273 (ptt90) REVERT: b 15 LYS cc_start: 0.8969 (pttp) cc_final: 0.8630 (mmtm) REVERT: b 26 TRP cc_start: 0.7919 (t60) cc_final: 0.7637 (t60) REVERT: b 32 MET cc_start: 0.8934 (mmp) cc_final: 0.8714 (mmm) REVERT: b 51 TYR cc_start: 0.8150 (m-80) cc_final: 0.7093 (t80) REVERT: b 52 ASN cc_start: 0.7294 (t0) cc_final: 0.6648 (m110) REVERT: b 53 TYR cc_start: 0.8387 (t80) cc_final: 0.7609 (t80) REVERT: q 68 MET cc_start: 0.6234 (ppp) cc_final: 0.5984 (ppp) REVERT: q 93 MET cc_start: 0.6850 (mtp) cc_final: 0.6476 (mtp) REVERT: q 142 THR cc_start: 0.8137 (m) cc_final: 0.7882 (p) REVERT: q 144 TYR cc_start: 0.5834 (m-80) cc_final: 0.5570 (m-80) REVERT: s 78 TYR cc_start: 0.5500 (m-80) cc_final: 0.5276 (m-80) REVERT: s 87 LEU cc_start: 0.7242 (pp) cc_final: 0.6900 (pp) outliers start: 137 outliers final: 72 residues processed: 1023 average time/residue: 0.2046 time to fit residues: 344.6559 Evaluate side-chains 925 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 844 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 222 MET 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 59 TYR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 155 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 71 VAL 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 281 ILE 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 650 SER 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 138 GLN Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 156 MET 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 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 165 ASP Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain P residue 51 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 64 LYS 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 V residue 19 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 89 LEU 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 a residue 17 VAL Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 69 HIS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 373 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 229 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 353 optimal weight: 0.9980 chunk 385 optimal weight: 0.5980 chunk 192 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** 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 ** 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 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 T 101 ASN V 111 GLN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 HIS q 17 HIS 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 = 0.3846 r_free = 0.3846 target = 0.107409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.085925 restraints weight = 100900.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.088148 restraints weight = 47612.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090504 restraints weight = 28006.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.090213 restraints weight = 21497.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.090351 restraints weight = 20356.549| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 34767 Z= 0.150 Angle : 0.924 77.454 47131 Z= 0.363 Chirality : 0.046 0.255 5134 Planarity : 0.005 0.126 5962 Dihedral : 9.015 171.213 4952 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.19 % Rotamer: Outliers : 3.84 % Allowed : 23.07 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4121 helix: 0.63 (0.12), residues: 1878 sheet: -0.95 (0.27), residues: 371 loop : -0.96 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 655 TYR 0.025 0.002 TYR W 126 PHE 0.022 0.002 PHE D 174 TRP 0.062 0.002 TRP F 62 HIS 0.026 0.001 HIS q 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (34726) covalent geometry : angle 0.71819 / 0.36 (47039) SS BOND : bond 0.00188 / 0.10 ( 4) SS BOND : angle 0.46168 / 0.25 ( 8) hydrogen bonds : bond 0.04277 / 2.81 ( 1411) hydrogen bonds : angle 5.04350 / 3.59 ( 4116) metal coordination : bond 0.01545 / 0.92 ( 37) metal coordination : angle 13.78504 / 10.25 ( 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 1063 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 924 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8320 (mpp) cc_final: 0.7592 (tpp) REVERT: B 107 MET cc_start: 0.8281 (ttm) cc_final: 0.7837 (tpp) REVERT: B 122 ARG cc_start: 0.8737 (pmt170) cc_final: 0.8350 (ttt180) REVERT: B 147 LYS cc_start: 0.8871 (mttt) cc_final: 0.8404 (ttpt) REVERT: B 150 ASP cc_start: 0.9012 (m-30) cc_final: 0.8739 (m-30) REVERT: B 157 TYR cc_start: 0.8311 (m-80) cc_final: 0.7695 (m-80) REVERT: B 176 SER cc_start: 0.9027 (m) cc_final: 0.8719 (t) REVERT: B 185 VAL cc_start: 0.9255 (m) cc_final: 0.9044 (p) REVERT: B 220 ILE cc_start: 0.9181 (tp) cc_final: 0.8928 (tp) REVERT: C 117 ASP cc_start: 0.8426 (t0) cc_final: 0.8221 (t0) REVERT: C 148 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: C 149 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9408 (pp) REVERT: C 207 VAL cc_start: 0.9543 (m) cc_final: 0.9305 (p) REVERT: C 224 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: D 80 MET cc_start: 0.7119 (mmp) cc_final: 0.6758 (ttp) REVERT: D 201 PHE cc_start: 0.8470 (m-80) cc_final: 0.8266 (m-80) REVERT: D 205 GLU cc_start: 0.8038 (tp30) cc_final: 0.7643 (tp30) REVERT: D 371 MET cc_start: 0.9031 (ptm) cc_final: 0.8707 (ttp) REVERT: D 443 MET cc_start: 0.8672 (mpp) cc_final: 0.8266 (mpp) REVERT: E 105 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8464 (pm20) REVERT: E 113 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7406 (mt-10) REVERT: E 123 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7080 (mtp180) REVERT: E 194 ASP cc_start: 0.7360 (t0) cc_final: 0.7069 (t0) REVERT: F 77 LEU cc_start: 0.9052 (tt) cc_final: 0.8812 (pp) REVERT: F 131 MET cc_start: 0.8382 (ptm) cc_final: 0.8059 (ppp) REVERT: F 209 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7971 (mp0) REVERT: G 42 MET cc_start: 0.9304 (mmm) cc_final: 0.9045 (mmm) REVERT: G 77 MET cc_start: 0.8856 (tpp) cc_final: 0.8572 (tpp) REVERT: G 136 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7524 (mt-10) REVERT: G 138 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7938 (t0) REVERT: G 264 SER cc_start: 0.9256 (m) cc_final: 0.8869 (p) REVERT: G 396 GLU cc_start: 0.8147 (tt0) cc_final: 0.7736 (tp30) REVERT: G 605 GLN cc_start: 0.7915 (pp30) cc_final: 0.7551 (pp30) REVERT: G 608 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8511 (m) REVERT: G 618 GLU cc_start: 0.8676 (mp0) cc_final: 0.8292 (mp0) REVERT: G 648 GLU cc_start: 0.8121 (tp30) cc_final: 0.7345 (tp30) REVERT: G 707 MET cc_start: 0.9283 (mmm) cc_final: 0.9081 (mmm) REVERT: H 15 ILE cc_start: 0.9198 (mm) cc_final: 0.8966 (mt) REVERT: H 43 TYR cc_start: 0.8785 (m-80) cc_final: 0.8255 (m-10) REVERT: H 54 LYS cc_start: 0.9148 (ptmm) cc_final: 0.8832 (ptmm) REVERT: H 86 TRP cc_start: 0.8376 (m100) cc_final: 0.8175 (m100) REVERT: H 172 MET cc_start: 0.7864 (ppp) cc_final: 0.7574 (ppp) REVERT: H 173 TRP cc_start: 0.8089 (m-10) cc_final: 0.7483 (m-90) REVERT: H 181 MET cc_start: 0.8851 (mtt) cc_final: 0.8266 (mtt) REVERT: H 184 MET cc_start: 0.8757 (mmt) cc_final: 0.8329 (mmt) REVERT: H 234 MET cc_start: 0.9105 (mmm) cc_final: 0.8704 (mmm) REVERT: H 247 TYR cc_start: 0.8053 (t80) cc_final: 0.7758 (t80) REVERT: H 282 TYR cc_start: 0.7761 (t80) cc_final: 0.6949 (t80) REVERT: H 286 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8459 (mpp) REVERT: H 292 ASN cc_start: 0.8205 (m-40) cc_final: 0.7888 (m-40) REVERT: I 55 ASP cc_start: 0.8276 (m-30) cc_final: 0.7860 (t70) REVERT: I 76 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7423 (t80) REVERT: I 94 SER cc_start: 0.8591 (p) cc_final: 0.8359 (p) REVERT: I 191 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8417 (tt) REVERT: I 208 ASP cc_start: 0.8252 (t0) cc_final: 0.7715 (t70) REVERT: P 79 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8591 (mt0) REVERT: P 97 MET cc_start: 0.7769 (ptp) cc_final: 0.7417 (ptp) REVERT: P 283 MET cc_start: 0.7719 (mmp) cc_final: 0.5971 (tpp) REVERT: P 328 MET cc_start: 0.7354 (mmm) cc_final: 0.7065 (mmm) REVERT: Q 99 MET cc_start: 0.9106 (ptp) cc_final: 0.8820 (ptp) REVERT: Q 128 PHE cc_start: 0.8434 (m-80) cc_final: 0.7940 (m-80) REVERT: Q 164 PHE cc_start: 0.8400 (m-80) cc_final: 0.7535 (m-80) REVERT: Q 166 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.7507 (t-100) REVERT: R 73 GLU cc_start: 0.8232 (pm20) cc_final: 0.7529 (mp0) REVERT: R 74 HIS cc_start: 0.7694 (t-90) cc_final: 0.7081 (t-170) REVERT: R 80 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7438 (t0) REVERT: R 106 TYR cc_start: 0.9045 (m-80) cc_final: 0.8648 (m-80) REVERT: S 40 ARG cc_start: 0.9031 (mtt180) cc_final: 0.8654 (mtm180) REVERT: S 45 LYS cc_start: 0.9117 (tptt) cc_final: 0.8860 (mmmt) REVERT: T 80 LYS cc_start: 0.8846 (mttt) cc_final: 0.8587 (mmtt) REVERT: T 117 GLU cc_start: 0.7764 (pp20) cc_final: 0.7372 (pp20) REVERT: T 118 ILE cc_start: 0.8848 (mm) cc_final: 0.8622 (mm) REVERT: T 129 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7182 (tp30) REVERT: V 97 TRP cc_start: 0.7717 (m-10) cc_final: 0.7413 (m-10) REVERT: W 45 GLU cc_start: 0.8543 (tp30) cc_final: 0.7979 (tp30) REVERT: W 56 ASP cc_start: 0.8876 (t0) cc_final: 0.7877 (t0) REVERT: W 61 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8561 (mm-40) REVERT: W 69 MET cc_start: 0.8787 (mmt) cc_final: 0.8536 (mmt) REVERT: W 109 PHE cc_start: 0.8733 (m-80) cc_final: 0.8520 (m-80) REVERT: W 129 HIS cc_start: 0.7113 (m90) cc_final: 0.6902 (m90) REVERT: X 44 MET cc_start: 0.8850 (tpp) cc_final: 0.8541 (mtp) REVERT: Z 65 LEU cc_start: 0.9220 (mt) cc_final: 0.8864 (mt) REVERT: Z 69 ILE cc_start: 0.8689 (mt) cc_final: 0.8462 (mt) REVERT: Z 76 GLN cc_start: 0.8517 (tp40) cc_final: 0.8300 (tp-100) REVERT: a 45 TRP cc_start: 0.8572 (t60) cc_final: 0.8312 (t60) REVERT: a 53 ARG cc_start: 0.8441 (mtm110) cc_final: 0.7934 (ttt-90) REVERT: b 15 LYS cc_start: 0.8964 (pttp) cc_final: 0.8607 (mmtm) REVERT: b 43 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7949 (m) REVERT: b 51 TYR cc_start: 0.8215 (m-80) cc_final: 0.7065 (t80) REVERT: b 52 ASN cc_start: 0.7167 (t0) cc_final: 0.6426 (m110) REVERT: b 53 TYR cc_start: 0.8610 (t80) cc_final: 0.7862 (t80) REVERT: q 58 ARG cc_start: 0.6968 (ttt180) cc_final: 0.5979 (ttt180) REVERT: q 68 MET cc_start: 0.6321 (ppp) cc_final: 0.6060 (ppp) REVERT: q 144 TYR cc_start: 0.5938 (m-80) cc_final: 0.5671 (m-80) REVERT: s 87 LEU cc_start: 0.7219 (pp) cc_final: 0.6915 (pp) outliers start: 139 outliers final: 78 residues processed: 999 average time/residue: 0.1924 time to fit residues: 318.8508 Evaluate side-chains 927 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 836 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 93 MET 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 C residue 66 GLU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 224 GLU 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 105 GLN Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 294 VAL 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 341 ILE Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 543 LYS 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 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 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 Q residue 59 LEU 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 93 ILE 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 T residue 81 ASP Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 128 PHE Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 97 ILE 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 87 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 43 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 31 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 214 optimal weight: 3.9990 chunk 379 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 366 optimal weight: 0.0170 chunk 147 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN C 104 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN W 73 ASN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 17 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 = 0.3815 r_free = 0.3815 target = 0.105600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083927 restraints weight = 104357.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.085494 restraints weight = 45430.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.086570 restraints weight = 31293.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.086356 restraints weight = 26237.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086507 restraints weight = 25714.985| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.6371 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= 0.186 Angle : 0.951 81.141 47131 Z= 0.369 Chirality : 0.046 0.250 5134 Planarity : 0.005 0.128 5962 Dihedral : 8.997 160.962 4952 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 3.98 % Allowed : 23.90 % Favored : 72.12 % 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: -0.33 (0.13), residues: 4121 helix: 0.69 (0.12), residues: 1884 sheet: -0.93 (0.27), residues: 383 loop : -0.95 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG W 26 TYR 0.029 0.002 TYR W 126 PHE 0.035 0.002 PHE B 117 TRP 0.061 0.002 TRP F 62 HIS 0.033 0.002 HIS q 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (34726) covalent geometry : angle 0.72840 / 0.37 (47039) SS BOND : bond 0.00203 / 0.10 ( 4) SS BOND : angle 0.35689 / 0.19 ( 8) hydrogen bonds : bond 0.04227 / 2.78 ( 1411) hydrogen bonds : angle 5.03788 / 3.59 ( 4116) metal coordination : bond 0.02102 / 1.21 ( 37) metal coordination : angle 14.50795 / 10.72 ( 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 1004 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 860 time to evaluate : 1.351 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: B 103 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8207 (mm-30) REVERT: B 122 ARG cc_start: 0.8634 (pmt170) cc_final: 0.8301 (tpt170) REVERT: B 147 LYS cc_start: 0.8914 (mttt) cc_final: 0.8418 (ttpt) REVERT: B 150 ASP cc_start: 0.8959 (m-30) cc_final: 0.8733 (m-30) REVERT: B 157 TYR cc_start: 0.8352 (m-80) cc_final: 0.8096 (m-80) REVERT: B 176 SER cc_start: 0.9121 (m) cc_final: 0.8846 (t) REVERT: B 220 ILE cc_start: 0.9222 (tp) cc_final: 0.8973 (tp) REVERT: C 117 ASP cc_start: 0.8582 (t0) cc_final: 0.8304 (t0) REVERT: C 149 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9322 (pp) REVERT: D 105 MET cc_start: 0.7363 (tmm) cc_final: 0.6908 (tpt) REVERT: D 201 PHE cc_start: 0.8538 (m-80) cc_final: 0.8331 (m-80) REVERT: D 205 GLU cc_start: 0.8120 (tp30) cc_final: 0.7490 (tp30) REVERT: D 292 MET cc_start: 0.8869 (mmm) cc_final: 0.8292 (mmt) REVERT: D 443 MET cc_start: 0.8750 (mpp) cc_final: 0.8222 (mpp) REVERT: E 83 ASP cc_start: 0.9221 (t0) cc_final: 0.8710 (m-30) REVERT: E 105 GLN cc_start: 0.8952 (pt0) cc_final: 0.8566 (pm20) REVERT: E 113 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7544 (mt-10) REVERT: E 123 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7068 (mtp180) REVERT: E 124 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7903 (ttpt) REVERT: E 184 MET cc_start: 0.6993 (ptp) cc_final: 0.6275 (ptt) REVERT: E 194 ASP cc_start: 0.7304 (t0) cc_final: 0.6664 (p0) REVERT: F 131 MET cc_start: 0.8307 (ptm) cc_final: 0.7709 (ppp) REVERT: F 209 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8076 (mp0) REVERT: F 413 TRP cc_start: 0.8205 (t60) cc_final: 0.7839 (t60) REVERT: G 77 MET cc_start: 0.8890 (tpp) cc_final: 0.8634 (tpp) REVERT: G 94 MET cc_start: 0.8681 (tpt) cc_final: 0.8170 (tpp) REVERT: G 97 MET cc_start: 0.6096 (mtm) cc_final: 0.5824 (mtm) REVERT: G 138 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.8004 (t0) REVERT: G 264 SER cc_start: 0.9342 (m) cc_final: 0.8880 (p) REVERT: G 306 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7848 (ttm) REVERT: G 396 GLU cc_start: 0.8198 (tt0) cc_final: 0.7773 (tp30) REVERT: G 605 GLN cc_start: 0.8004 (pp30) cc_final: 0.7616 (pp30) REVERT: G 608 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8552 (m) REVERT: G 618 GLU cc_start: 0.8668 (mp0) cc_final: 0.8284 (mp0) REVERT: G 628 GLU cc_start: 0.8624 (tt0) cc_final: 0.8397 (tt0) REVERT: G 648 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: G 707 MET cc_start: 0.9370 (mmm) cc_final: 0.9140 (mmm) REVERT: H 15 ILE cc_start: 0.9204 (mm) cc_final: 0.8970 (mt) REVERT: H 54 LYS cc_start: 0.9169 (ptmm) cc_final: 0.8835 (ptmm) REVERT: H 86 TRP cc_start: 0.8624 (m100) cc_final: 0.8301 (m100) REVERT: H 134 ARG cc_start: 0.8819 (mtm180) cc_final: 0.8511 (mtm180) REVERT: H 172 MET cc_start: 0.8070 (ppp) cc_final: 0.7750 (ppp) REVERT: H 173 TRP cc_start: 0.8122 (m-10) cc_final: 0.7542 (m-90) REVERT: H 181 MET cc_start: 0.8878 (mtt) cc_final: 0.8371 (mtt) REVERT: H 183 MET cc_start: 0.9249 (mtp) cc_final: 0.8714 (mtt) REVERT: H 184 MET cc_start: 0.8831 (mmt) cc_final: 0.8423 (mmt) REVERT: H 225 MET cc_start: 0.9093 (mmm) cc_final: 0.8696 (mmt) REVERT: H 234 MET cc_start: 0.9133 (mmm) cc_final: 0.8670 (mmm) REVERT: H 282 TYR cc_start: 0.7743 (t80) cc_final: 0.6969 (t80) REVERT: H 286 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.8456 (mpp) REVERT: H 292 ASN cc_start: 0.8361 (m-40) cc_final: 0.8037 (m-40) REVERT: I 55 ASP cc_start: 0.8392 (m-30) cc_final: 0.7919 (t70) REVERT: I 63 TRP cc_start: 0.8902 (m-90) cc_final: 0.8514 (m-90) REVERT: I 76 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7447 (t80) REVERT: I 94 SER cc_start: 0.8580 (p) cc_final: 0.8323 (p) REVERT: I 117 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8835 (mtpp) REVERT: I 191 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8540 (tt) REVERT: I 208 ASP cc_start: 0.8397 (t0) cc_final: 0.7884 (t70) REVERT: P 97 MET cc_start: 0.7733 (ptp) cc_final: 0.7404 (ptp) REVERT: P 283 MET cc_start: 0.7663 (mmp) cc_final: 0.5918 (tpp) REVERT: P 298 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7250 (t80) REVERT: P 328 MET cc_start: 0.7229 (mmm) cc_final: 0.6943 (mmm) REVERT: Q 128 PHE cc_start: 0.8665 (m-80) cc_final: 0.8371 (m-80) REVERT: Q 166 TRP cc_start: 0.7924 (OUTLIER) cc_final: 0.6526 (m100) REVERT: R 73 GLU cc_start: 0.8387 (pm20) cc_final: 0.8097 (pm20) REVERT: R 80 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7677 (t0) REVERT: R 106 TYR cc_start: 0.9044 (m-80) cc_final: 0.8791 (m-80) REVERT: S 40 ARG cc_start: 0.9157 (mtt180) cc_final: 0.8675 (mtm180) REVERT: S 45 LYS cc_start: 0.9169 (tptt) cc_final: 0.8910 (mmmt) REVERT: T 80 LYS cc_start: 0.8878 (mttt) cc_final: 0.8671 (tmtt) REVERT: T 118 ILE cc_start: 0.9003 (mm) cc_final: 0.8751 (mm) REVERT: T 130 ILE cc_start: 0.7953 (mm) cc_final: 0.7638 (tt) REVERT: V 53 ASN cc_start: 0.8835 (m-40) cc_final: 0.8516 (m-40) REVERT: W 24 PHE cc_start: 0.8560 (m-80) cc_final: 0.8334 (m-80) REVERT: W 45 GLU cc_start: 0.8621 (tp30) cc_final: 0.7963 (tp30) REVERT: W 56 ASP cc_start: 0.8399 (t0) cc_final: 0.8133 (t0) REVERT: W 61 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8589 (mm-40) REVERT: W 69 MET cc_start: 0.8840 (mmt) cc_final: 0.8637 (mmt) REVERT: W 92 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8415 (mm-30) REVERT: W 95 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7736 (mt-10) REVERT: X 32 TYR cc_start: 0.8481 (t80) cc_final: 0.8217 (t80) REVERT: X 43 PHE cc_start: 0.8326 (t80) cc_final: 0.8041 (t80) REVERT: X 44 MET cc_start: 0.9072 (tpp) cc_final: 0.8652 (mtp) REVERT: Z 65 LEU cc_start: 0.9316 (mt) cc_final: 0.8853 (mt) REVERT: Z 69 ILE cc_start: 0.8904 (mt) cc_final: 0.8680 (mt) REVERT: a 53 ARG cc_start: 0.8462 (mtm110) cc_final: 0.7948 (ttt-90) REVERT: b 15 LYS cc_start: 0.9009 (pttp) cc_final: 0.8641 (mmtm) REVERT: b 44 MET cc_start: 0.8612 (ptp) cc_final: 0.8185 (ptp) REVERT: b 51 TYR cc_start: 0.8163 (m-80) cc_final: 0.7050 (t80) REVERT: b 53 TYR cc_start: 0.8786 (t80) cc_final: 0.8294 (t80) outliers start: 144 outliers final: 92 residues processed: 934 average time/residue: 0.2012 time to fit residues: 311.3348 Evaluate side-chains 903 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 798 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 146 CYS 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 E residue 39 VAL Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 123 ARG 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 F residue 169 LEU Chi-restraints excluded: chain F residue 294 VAL 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 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 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 640 ASP Chi-restraints excluded: chain G residue 648 GLU 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 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 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 100 GLU 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 88 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 272 LEU 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 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 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 S residue 85 ASP 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 T residue 123 GLU Chi-restraints excluded: chain T residue 124 ASP Chi-restraints excluded: chain V residue 31 THR 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 69 ASN 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 17 VAL Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain a residue 54 ILE 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 92 LYS Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 106 LEU 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: 6.9990 chunk 127 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 393 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 391 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 245 optimal weight: 0.8980 chunk 405 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS B 151 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 HIS ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 275 HIS Q 109 ASN ** R 56 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** ** q 17 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.102034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080657 restraints weight = 102978.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081649 restraints weight = 46414.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.083005 restraints weight = 31896.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.083002 restraints weight = 26789.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.083161 restraints weight = 25241.166| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 34767 Z= 0.238 Angle : 1.005 83.416 47131 Z= 0.391 Chirality : 0.048 0.336 5134 Planarity : 0.006 0.131 5962 Dihedral : 8.960 142.385 4952 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 4.45 % Allowed : 23.98 % Favored : 71.57 % 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: 0.69 (0.12), residues: 1880 sheet: -0.87 (0.26), residues: 397 loop : -0.94 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 111 TYR 0.029 0.002 TYR B 203 PHE 0.027 0.002 PHE P 288 TRP 0.068 0.003 TRP F 62 HIS 0.052 0.002 HIS q 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (34726) covalent geometry : angle 0.76868 / 0.39 (47039) SS BOND : bond 0.00211 / 0.11 ( 4) SS BOND : angle 0.41741 / 0.24 ( 8) hydrogen bonds : bond 0.04367 / 2.87 ( 1411) hydrogen bonds : angle 5.13863 / 3.66 ( 4116) metal coordination : bond 0.02873 / 1.64 ( 37) metal coordination : angle 15.36547 / 11.25 ( 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 970 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 809 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: B 103 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8170 (mm-30) REVERT: B 122 ARG cc_start: 0.8571 (pmt170) cc_final: 0.8355 (tpt170) REVERT: B 147 LYS cc_start: 0.8927 (mttt) cc_final: 0.8378 (ttpt) REVERT: B 157 TYR cc_start: 0.8488 (m-80) cc_final: 0.8230 (m-80) REVERT: B 220 ILE cc_start: 0.9206 (tp) cc_final: 0.8947 (tp) REVERT: C 117 ASP cc_start: 0.8539 (t0) cc_final: 0.8261 (t0) REVERT: C 149 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9381 (pp) REVERT: D 80 MET cc_start: 0.7126 (mmp) cc_final: 0.6625 (ttp) REVERT: D 105 MET cc_start: 0.7872 (tmm) cc_final: 0.7575 (tpt) REVERT: D 205 GLU cc_start: 0.8209 (tp30) cc_final: 0.7724 (tp30) REVERT: D 292 MET cc_start: 0.8899 (mmm) cc_final: 0.8342 (mmt) REVERT: E 98 ASN cc_start: 0.9065 (m-40) cc_final: 0.8607 (m110) REVERT: E 105 GLN cc_start: 0.9014 (pt0) cc_final: 0.8656 (pm20) REVERT: E 113 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7540 (mt-10) REVERT: E 123 ARG cc_start: 0.7386 (mtp180) cc_final: 0.7134 (mtp180) REVERT: E 124 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7908 (ttpt) REVERT: F 209 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8043 (mp0) REVERT: F 377 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7545 (tp30) REVERT: F 413 TRP cc_start: 0.8305 (t60) cc_final: 0.8071 (t60) REVERT: G 42 MET cc_start: 0.9360 (mmm) cc_final: 0.9117 (mmm) REVERT: G 77 MET cc_start: 0.8933 (tpp) cc_final: 0.8713 (tpp) REVERT: G 94 MET cc_start: 0.8713 (tpt) cc_final: 0.8301 (tpp) REVERT: G 97 MET cc_start: 0.6389 (mtm) cc_final: 0.6080 (mtm) REVERT: G 138 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8073 (t0) REVERT: G 264 SER cc_start: 0.9367 (m) cc_final: 0.8915 (p) REVERT: G 306 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7955 (ttm) REVERT: G 396 GLU cc_start: 0.8286 (tt0) cc_final: 0.7867 (tp30) REVERT: G 605 GLN cc_start: 0.8012 (pp30) cc_final: 0.7721 (pp30) REVERT: G 608 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8641 (m) REVERT: G 618 GLU cc_start: 0.8678 (mp0) cc_final: 0.8277 (mp0) REVERT: G 628 GLU cc_start: 0.8626 (tt0) cc_final: 0.8393 (tt0) REVERT: G 707 MET cc_start: 0.9377 (mmm) cc_final: 0.9165 (mmm) REVERT: H 15 ILE cc_start: 0.9242 (mm) cc_final: 0.9028 (mt) REVERT: H 54 LYS cc_start: 0.9200 (ptmm) cc_final: 0.8552 (ptmt) REVERT: H 58 LYS cc_start: 0.9011 (tppp) cc_final: 0.8494 (tptp) REVERT: H 134 ARG cc_start: 0.8834 (mtm180) cc_final: 0.8546 (mtm180) REVERT: H 173 TRP cc_start: 0.8143 (m-10) cc_final: 0.7668 (m-90) REVERT: H 183 MET cc_start: 0.9267 (mtp) cc_final: 0.8971 (mtt) REVERT: H 184 MET cc_start: 0.8901 (mmt) cc_final: 0.8451 (mmt) REVERT: H 225 MET cc_start: 0.9042 (mmm) cc_final: 0.8576 (mmt) REVERT: H 234 MET cc_start: 0.9218 (mmm) cc_final: 0.8820 (mmm) REVERT: H 282 TYR cc_start: 0.7873 (t80) cc_final: 0.7141 (t80) REVERT: H 286 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8302 (mpp) REVERT: H 292 ASN cc_start: 0.8442 (m-40) cc_final: 0.8153 (m-40) REVERT: I 63 TRP cc_start: 0.8933 (m-10) cc_final: 0.8682 (m-90) REVERT: I 76 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7580 (t80) REVERT: I 94 SER cc_start: 0.8612 (p) cc_final: 0.8295 (p) REVERT: I 117 LYS cc_start: 0.9126 (mtmt) cc_final: 0.8878 (mtpp) REVERT: I 191 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8604 (tt) REVERT: I 208 ASP cc_start: 0.8451 (t0) cc_final: 0.8041 (t70) REVERT: P 97 MET cc_start: 0.7832 (ptp) cc_final: 0.7495 (ptp) REVERT: P 283 MET cc_start: 0.8077 (mmp) cc_final: 0.6508 (tpp) REVERT: P 298 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.7234 (t80) REVERT: P 328 MET cc_start: 0.7436 (mmm) cc_final: 0.7183 (mmm) REVERT: Q 96 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8360 (mttp) REVERT: Q 128 PHE cc_start: 0.8810 (m-80) cc_final: 0.8378 (m-10) REVERT: R 45 ARG cc_start: 0.2749 (ptt180) cc_final: 0.2246 (tmm-80) REVERT: R 80 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7846 (t0) REVERT: S 40 ARG cc_start: 0.9127 (mtt180) cc_final: 0.8564 (mtm180) REVERT: S 45 LYS cc_start: 0.9175 (tptt) cc_final: 0.8929 (mmmt) REVERT: S 58 CYS cc_start: 0.6796 (m) cc_final: 0.6485 (m) REVERT: T 80 LYS cc_start: 0.8911 (mttt) cc_final: 0.8707 (tmtt) REVERT: T 117 GLU cc_start: 0.8040 (pp20) cc_final: 0.7641 (pp20) REVERT: T 118 ILE cc_start: 0.8906 (mm) cc_final: 0.8668 (mm) REVERT: T 129 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7215 (tp30) REVERT: T 130 ILE cc_start: 0.8032 (mm) cc_final: 0.7200 (tt) REVERT: V 53 ASN cc_start: 0.8845 (m-40) cc_final: 0.8480 (m-40) REVERT: W 24 PHE cc_start: 0.8704 (m-80) cc_final: 0.8426 (m-80) REVERT: W 61 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8624 (mm-40) REVERT: W 69 MET cc_start: 0.8971 (mmt) cc_final: 0.8765 (mmt) REVERT: W 93 LEU cc_start: 0.9350 (tt) cc_final: 0.9048 (tt) REVERT: W 95 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8295 (mt-10) REVERT: W 109 PHE cc_start: 0.8880 (m-80) cc_final: 0.8545 (m-80) REVERT: X 43 PHE cc_start: 0.8435 (t80) cc_final: 0.8210 (t80) REVERT: X 44 MET cc_start: 0.9123 (tpp) cc_final: 0.8717 (mtp) REVERT: X 111 VAL cc_start: 0.8620 (p) cc_final: 0.8384 (m) REVERT: Z 65 LEU cc_start: 0.9365 (mt) cc_final: 0.9100 (mm) REVERT: Z 75 PHE cc_start: 0.9530 (m-10) cc_final: 0.9260 (m-10) REVERT: Z 76 GLN cc_start: 0.8981 (tp40) cc_final: 0.8620 (tp40) REVERT: a 53 ARG cc_start: 0.8486 (mtm110) cc_final: 0.7933 (ttt-90) REVERT: a 60 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.7870 (p90) REVERT: a 61 TYR cc_start: 0.7200 (m-80) cc_final: 0.6896 (m-80) REVERT: b 15 LYS cc_start: 0.9030 (pttp) cc_final: 0.8714 (mmtm) REVERT: b 32 MET cc_start: 0.8547 (mmm) cc_final: 0.7949 (tpt) REVERT: b 51 TYR cc_start: 0.8194 (m-80) cc_final: 0.7050 (t80) REVERT: b 53 TYR cc_start: 0.8943 (t80) cc_final: 0.8360 (t80) outliers start: 161 outliers final: 114 residues processed: 898 average time/residue: 0.2080 time to fit residues: 308.6841 Evaluate side-chains 902 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 774 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 13 LEU 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 93 MET Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 130 VAL 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 120 THR 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 D residue 98 VAL Chi-restraints excluded: chain D residue 146 CYS 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 E residue 54 PHE Chi-restraints excluded: chain E residue 124 LYS 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 203 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 377 GLU Chi-restraints excluded: chain F residue 435 VAL Chi-restraints excluded: chain G residue 100 TRP 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 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 640 ASP 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 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 200 LEU 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 314 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 100 GLU 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 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 272 LEU 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 54 THR 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 93 ILE 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 123 GLU Chi-restraints excluded: chain T residue 124 ASP 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 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 128 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 135 ARG Chi-restraints excluded: chain Z residue 43 LEU 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 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain b residue 19 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 66 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 q residue 142 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 403 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS B 151 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.106093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085196 restraints weight = 103279.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.086562 restraints weight = 43954.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.087343 restraints weight = 30914.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087736 restraints weight = 25668.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087756 restraints weight = 24636.541| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 34767 Z= 0.146 Angle : 0.965 81.302 47131 Z= 0.371 Chirality : 0.046 0.307 5134 Planarity : 0.005 0.129 5962 Dihedral : 8.736 137.619 4952 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 2.93 % Allowed : 26.17 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4121 helix: 0.77 (0.12), residues: 1879 sheet: -0.87 (0.27), residues: 380 loop : -0.91 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 26 TYR 0.030 0.002 TYR B 203 PHE 0.037 0.002 PHE q 74 TRP 0.062 0.002 TRP b 26 HIS 0.012 0.001 HIS q 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (34726) covalent geometry : angle 0.74282 / 0.37 (47039) SS BOND : bond 0.00152 / 0.08 ( 4) SS BOND : angle 0.34158 / 0.18 ( 8) hydrogen bonds : bond 0.04104 / 2.70 ( 1411) hydrogen bonds : angle 5.01757 / 3.57 ( 4116) metal coordination : bond 0.01439 / 0.91 ( 37) metal coordination : angle 14.62021 / 10.75 ( 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 957 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 851 time to evaluate : 1.323 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: A 53 MET cc_start: 0.8383 (mpp) cc_final: 0.7694 (tpp) REVERT: B 77 LYS cc_start: 0.9010 (mttt) cc_final: 0.8628 (mttm) REVERT: B 122 ARG cc_start: 0.8474 (pmt170) cc_final: 0.8207 (tpt170) REVERT: B 147 LYS cc_start: 0.8856 (mttt) cc_final: 0.8297 (ttpt) REVERT: B 176 SER cc_start: 0.9168 (m) cc_final: 0.8933 (t) REVERT: B 220 ILE cc_start: 0.9163 (tp) cc_final: 0.8917 (tp) REVERT: C 117 ASP cc_start: 0.8535 (t0) cc_final: 0.8303 (t0) REVERT: C 149 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9343 (pp) REVERT: C 207 VAL cc_start: 0.9612 (m) cc_final: 0.9374 (p) REVERT: D 80 MET cc_start: 0.7142 (mmp) cc_final: 0.6532 (ttp) REVERT: D 205 GLU cc_start: 0.8053 (tp30) cc_final: 0.7577 (tp30) REVERT: D 292 MET cc_start: 0.8813 (mmm) cc_final: 0.8359 (mmt) REVERT: E 80 PRO cc_start: 0.8679 (Cg_exo) cc_final: 0.8321 (Cg_endo) REVERT: E 105 GLN cc_start: 0.8981 (pt0) cc_final: 0.8658 (pm20) REVERT: E 113 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7424 (mt-10) REVERT: E 123 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7200 (mtp180) REVERT: E 124 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7664 (ttpt) REVERT: E 145 ASP cc_start: 0.9042 (t0) cc_final: 0.8828 (t0) REVERT: E 181 ASN cc_start: 0.7623 (t0) cc_final: 0.7303 (t0) REVERT: F 209 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8133 (mp0) REVERT: F 217 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8214 (tm-30) REVERT: F 276 PHE cc_start: 0.6631 (m-10) cc_final: 0.6422 (m-10) REVERT: F 377 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: F 386 ARG cc_start: 0.9026 (ttm110) cc_final: 0.8576 (ttp-110) REVERT: F 394 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8360 (mmtt) REVERT: F 448 ASP cc_start: 0.8617 (m-30) cc_final: 0.8413 (t0) REVERT: F 450 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8523 (mmt) REVERT: G 42 MET cc_start: 0.9321 (mmm) cc_final: 0.9107 (mmm) REVERT: G 77 MET cc_start: 0.8903 (tpp) cc_final: 0.8651 (tpp) REVERT: G 94 MET cc_start: 0.8680 (tpt) cc_final: 0.8272 (tpp) REVERT: G 97 MET cc_start: 0.6403 (mtm) cc_final: 0.6038 (mtm) REVERT: G 138 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8046 (t0) REVERT: G 264 SER cc_start: 0.9336 (m) cc_final: 0.8869 (p) REVERT: G 306 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.7928 (ttm) REVERT: G 396 GLU cc_start: 0.8226 (tt0) cc_final: 0.7848 (tp30) REVERT: G 605 GLN cc_start: 0.8044 (pp30) cc_final: 0.7755 (pp30) REVERT: G 608 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8545 (m) REVERT: G 618 GLU cc_start: 0.8655 (mp0) cc_final: 0.8268 (mp0) REVERT: G 628 GLU cc_start: 0.8609 (tt0) cc_final: 0.8339 (tt0) REVERT: G 707 MET cc_start: 0.9355 (mmm) cc_final: 0.9115 (mmm) REVERT: H 15 ILE cc_start: 0.9211 (mm) cc_final: 0.9004 (mt) REVERT: H 54 LYS cc_start: 0.9169 (ptmm) cc_final: 0.8566 (ptmt) REVERT: H 134 ARG cc_start: 0.8835 (mtm180) cc_final: 0.8538 (mtm180) REVERT: H 173 TRP cc_start: 0.8216 (m-10) cc_final: 0.7727 (m-90) REVERT: H 184 MET cc_start: 0.8863 (mmt) cc_final: 0.8423 (mmt) REVERT: H 224 PHE cc_start: 0.8599 (t80) cc_final: 0.7833 (t80) REVERT: H 225 MET cc_start: 0.9085 (mmm) cc_final: 0.8579 (mmt) REVERT: H 234 MET cc_start: 0.9182 (mmm) cc_final: 0.8803 (mmm) REVERT: H 247 TYR cc_start: 0.8108 (t80) cc_final: 0.7794 (t80) REVERT: H 282 TYR cc_start: 0.7657 (t80) cc_final: 0.6892 (t80) REVERT: H 286 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.8434 (mpp) REVERT: H 291 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7772 (mmmm) REVERT: H 292 ASN cc_start: 0.8210 (m-40) cc_final: 0.7975 (m-40) REVERT: I 76 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7677 (t80) REVERT: I 94 SER cc_start: 0.8839 (p) cc_final: 0.8568 (p) REVERT: I 117 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8784 (mtpp) REVERT: I 191 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8597 (tt) REVERT: I 208 ASP cc_start: 0.8461 (t0) cc_final: 0.8002 (t70) REVERT: P 97 MET cc_start: 0.7737 (ptp) cc_final: 0.7385 (ptp) REVERT: P 283 MET cc_start: 0.7872 (mmp) cc_final: 0.6359 (tpp) REVERT: P 298 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7101 (t80) REVERT: P 328 MET cc_start: 0.7411 (mmm) cc_final: 0.7150 (mmm) REVERT: Q 96 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8258 (mttp) REVERT: Q 99 MET cc_start: 0.9133 (ptp) cc_final: 0.8865 (ptp) REVERT: Q 128 PHE cc_start: 0.8680 (m-80) cc_final: 0.8414 (m-80) REVERT: Q 164 PHE cc_start: 0.8480 (m-10) cc_final: 0.8034 (m-10) REVERT: R 45 ARG cc_start: 0.2610 (ptt180) cc_final: 0.2142 (tmm-80) REVERT: R 73 GLU cc_start: 0.8377 (pm20) cc_final: 0.7310 (mp0) REVERT: R 80 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7728 (t0) REVERT: S 40 ARG cc_start: 0.9179 (mtt180) cc_final: 0.8699 (mtm180) REVERT: S 45 LYS cc_start: 0.9128 (tptt) cc_final: 0.8891 (mmmt) REVERT: S 58 CYS cc_start: 0.6701 (m) cc_final: 0.6452 (m) REVERT: T 129 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7394 (tp30) REVERT: T 130 ILE cc_start: 0.8040 (mm) cc_final: 0.7190 (tt) REVERT: V 53 ASN cc_start: 0.8814 (m-40) cc_final: 0.8427 (m-40) REVERT: W 24 PHE cc_start: 0.8748 (m-80) cc_final: 0.8264 (m-80) REVERT: W 45 GLU cc_start: 0.8548 (tp30) cc_final: 0.7894 (tp30) REVERT: W 54 GLN cc_start: 0.9033 (mt0) cc_final: 0.8456 (mp10) REVERT: W 61 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8631 (mm-40) REVERT: W 83 ASP cc_start: 0.8106 (t0) cc_final: 0.7863 (t0) REVERT: W 93 LEU cc_start: 0.9346 (tt) cc_final: 0.9034 (tt) REVERT: W 95 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8226 (mt-10) REVERT: W 109 PHE cc_start: 0.8831 (m-80) cc_final: 0.8470 (m-80) REVERT: X 43 PHE cc_start: 0.8394 (t80) cc_final: 0.8188 (t80) REVERT: X 44 MET cc_start: 0.9007 (tpp) cc_final: 0.8528 (mtp) REVERT: X 111 VAL cc_start: 0.8567 (p) cc_final: 0.8306 (m) REVERT: Z 65 LEU cc_start: 0.9412 (mt) cc_final: 0.9205 (mt) REVERT: Z 76 GLN cc_start: 0.8869 (tp40) cc_final: 0.8535 (tp40) REVERT: Z 98 MET cc_start: 0.1763 (mmt) cc_final: 0.1467 (mmt) REVERT: a 53 ARG cc_start: 0.8459 (mtm110) cc_final: 0.7931 (ttt-90) REVERT: b 8 PHE cc_start: 0.7400 (t80) cc_final: 0.7001 (t80) REVERT: b 15 LYS cc_start: 0.8997 (pttp) cc_final: 0.8642 (mmtm) REVERT: b 51 TYR cc_start: 0.8163 (m-80) cc_final: 0.7036 (t80) REVERT: b 53 TYR cc_start: 0.8698 (t80) cc_final: 0.8145 (t80) REVERT: q 58 ARG cc_start: 0.6208 (ttt180) cc_final: 0.5989 (ttt180) REVERT: q 132 LYS cc_start: 0.7186 (tmmt) cc_final: 0.6700 (tmmt) outliers start: 106 outliers final: 74 residues processed: 917 average time/residue: 0.1971 time to fit residues: 298.8675 Evaluate side-chains 885 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 797 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 377 GLU Chi-restraints excluded: chain F residue 435 VAL Chi-restraints excluded: chain F residue 450 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 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 640 ASP 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 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 213 VAL Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 289 LEU 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 103 LEU Chi-restraints excluded: chain I residue 129 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 259 VAL 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 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 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 123 GLU Chi-restraints excluded: chain T residue 124 ASP 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 78 GLU Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 66 VAL 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 r residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 2 optimal weight: 2.9990 chunk 390 optimal weight: 10.0000 chunk 183 optimal weight: 0.2980 chunk 322 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 394 optimal weight: 8.9990 chunk 227 optimal weight: 7.9990 chunk 91 optimal weight: 40.0000 chunk 312 optimal weight: 0.0970 chunk 203 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 178 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** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN W 129 HIS ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.105117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.084329 restraints weight = 103575.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.085472 restraints weight = 46015.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.086505 restraints weight = 32372.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086722 restraints weight = 26183.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.086874 restraints weight = 24946.799| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 34767 Z= 0.166 Angle : 0.978 81.614 47131 Z= 0.378 Chirality : 0.047 0.369 5134 Planarity : 0.005 0.129 5962 Dihedral : 8.617 128.999 4952 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 2.98 % Allowed : 26.31 % Favored : 70.71 % 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: -0.23 (0.13), residues: 4121 helix: 0.77 (0.12), residues: 1888 sheet: -0.91 (0.26), residues: 382 loop : -0.90 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 26 TYR 0.027 0.002 TYR I 86 PHE 0.029 0.002 PHE q 74 TRP 0.073 0.002 TRP b 26 HIS 0.011 0.001 HIS X 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (34726) covalent geometry : angle 0.75469 / 0.37 (47039) SS BOND : bond 0.00163 / 0.09 ( 4) SS BOND : angle 0.31173 / 0.17 ( 8) hydrogen bonds : bond 0.04072 / 2.69 ( 1411) hydrogen bonds : angle 5.02776 / 3.58 ( 4116) metal coordination : bond 0.01810 / 1.07 ( 37) metal coordination : angle 14.77165 / 10.87 ( 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 926 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 818 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8346 (mpp) cc_final: 0.7640 (tpp) REVERT: B 122 ARG cc_start: 0.8481 (pmt170) cc_final: 0.8198 (tpt170) REVERT: B 131 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7799 (ttt) REVERT: B 147 LYS cc_start: 0.8851 (mttt) cc_final: 0.8273 (ttpt) REVERT: B 176 SER cc_start: 0.9184 (m) cc_final: 0.8978 (t) REVERT: B 203 TYR cc_start: 0.8762 (t80) cc_final: 0.8554 (t80) REVERT: B 220 ILE cc_start: 0.9159 (tp) cc_final: 0.8914 (tp) REVERT: C 117 ASP cc_start: 0.8491 (t0) cc_final: 0.8228 (t0) REVERT: C 149 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9377 (pp) REVERT: C 207 VAL cc_start: 0.9609 (m) cc_final: 0.9378 (p) REVERT: D 80 MET cc_start: 0.7222 (mmp) cc_final: 0.6638 (ttp) REVERT: D 197 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8166 (ptm) REVERT: D 205 GLU cc_start: 0.8060 (tp30) cc_final: 0.7504 (tp30) REVERT: D 292 MET cc_start: 0.8788 (mmm) cc_final: 0.8387 (mmt) REVERT: E 59 TYR cc_start: 0.8722 (m-80) cc_final: 0.8159 (m-80) REVERT: E 97 MET cc_start: 0.8355 (mtm) cc_final: 0.8149 (mtm) REVERT: E 105 GLN cc_start: 0.8938 (pt0) cc_final: 0.8669 (pm20) REVERT: E 113 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7602 (mt-10) REVERT: E 123 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: E 124 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7568 (ttpt) REVERT: E 145 ASP cc_start: 0.9068 (t0) cc_final: 0.8578 (m-30) REVERT: E 181 ASN cc_start: 0.7595 (t0) cc_final: 0.7261 (t0) REVERT: F 209 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8167 (mp0) REVERT: F 217 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8253 (tm-30) REVERT: F 276 PHE cc_start: 0.6665 (m-10) cc_final: 0.6432 (m-10) REVERT: F 394 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8366 (mmtt) REVERT: G 42 MET cc_start: 0.9306 (mmm) cc_final: 0.9089 (mmm) REVERT: G 77 MET cc_start: 0.8890 (tpp) cc_final: 0.8681 (tpp) REVERT: G 94 MET cc_start: 0.8693 (tpt) cc_final: 0.8367 (tpp) REVERT: G 138 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8079 (t0) REVERT: G 264 SER cc_start: 0.9355 (m) cc_final: 0.8887 (p) REVERT: G 306 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7982 (ttm) REVERT: G 396 GLU cc_start: 0.8215 (tt0) cc_final: 0.7858 (tp30) REVERT: G 579 MET cc_start: 0.8322 (ptt) cc_final: 0.7804 (ppp) REVERT: G 605 GLN cc_start: 0.8065 (pp30) cc_final: 0.7794 (pp30) REVERT: G 608 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8547 (m) REVERT: G 618 GLU cc_start: 0.8669 (mp0) cc_final: 0.8271 (mp0) REVERT: G 628 GLU cc_start: 0.8528 (tt0) cc_final: 0.8284 (tt0) REVERT: G 707 MET cc_start: 0.9326 (mmm) cc_final: 0.9107 (mmm) REVERT: H 15 ILE cc_start: 0.9290 (mm) cc_final: 0.9045 (mt) REVERT: H 54 LYS cc_start: 0.9199 (ptmm) cc_final: 0.8681 (ptmt) REVERT: H 80 THR cc_start: 0.9601 (t) cc_final: 0.9311 (p) REVERT: H 134 ARG cc_start: 0.8877 (mtm180) cc_final: 0.8629 (mtm180) REVERT: H 173 TRP cc_start: 0.8242 (m-10) cc_final: 0.7734 (m-90) REVERT: H 184 MET cc_start: 0.8934 (mmt) cc_final: 0.8478 (mmt) REVERT: H 224 PHE cc_start: 0.8612 (t80) cc_final: 0.7902 (t80) REVERT: H 234 MET cc_start: 0.9164 (mmm) cc_final: 0.8786 (mmm) REVERT: H 247 TYR cc_start: 0.8099 (t80) cc_final: 0.7768 (t80) REVERT: H 282 TYR cc_start: 0.7638 (t80) cc_final: 0.7052 (t80) REVERT: H 286 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8321 (mpp) REVERT: H 292 ASN cc_start: 0.8192 (m-40) cc_final: 0.7903 (m110) REVERT: I 55 ASP cc_start: 0.8251 (m-30) cc_final: 0.7657 (t70) REVERT: I 76 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7729 (t80) REVERT: I 94 SER cc_start: 0.8810 (p) cc_final: 0.8477 (p) REVERT: I 117 LYS cc_start: 0.9281 (mtmt) cc_final: 0.9054 (mtpp) REVERT: I 191 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8599 (tt) REVERT: I 208 ASP cc_start: 0.8456 (t0) cc_final: 0.8018 (t70) REVERT: P 97 MET cc_start: 0.7790 (ptp) cc_final: 0.7507 (ptp) REVERT: P 283 MET cc_start: 0.7914 (mmp) cc_final: 0.6504 (tpp) REVERT: P 298 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7047 (t80) REVERT: P 328 MET cc_start: 0.7471 (mmm) cc_final: 0.7210 (mmm) REVERT: Q 96 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8282 (mttp) REVERT: Q 99 MET cc_start: 0.9130 (ptp) cc_final: 0.8859 (ptp) REVERT: Q 128 PHE cc_start: 0.8722 (m-80) cc_final: 0.8432 (m-80) REVERT: Q 164 PHE cc_start: 0.8516 (m-10) cc_final: 0.8114 (m-10) REVERT: R 45 ARG cc_start: 0.2527 (ptt180) cc_final: 0.2074 (tmm-80) REVERT: R 73 GLU cc_start: 0.8394 (pm20) cc_final: 0.8049 (pm20) REVERT: R 80 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7748 (t0) REVERT: S 40 ARG cc_start: 0.9161 (mtt180) cc_final: 0.8916 (mtm-85) REVERT: S 45 LYS cc_start: 0.9127 (tptt) cc_final: 0.8890 (mmmt) REVERT: S 58 CYS cc_start: 0.6728 (m) cc_final: 0.6496 (m) REVERT: T 129 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7538 (tp30) REVERT: T 130 ILE cc_start: 0.7996 (mm) cc_final: 0.7565 (mm) REVERT: T 139 MET cc_start: 0.6937 (tpp) cc_final: 0.6600 (tpp) REVERT: V 53 ASN cc_start: 0.8791 (m-40) cc_final: 0.8395 (m-40) REVERT: W 24 PHE cc_start: 0.8732 (m-80) cc_final: 0.8245 (m-80) REVERT: W 45 GLU cc_start: 0.8524 (tp30) cc_final: 0.7907 (tp30) REVERT: W 54 GLN cc_start: 0.9065 (mt0) cc_final: 0.8488 (mp10) REVERT: W 61 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8643 (mm-40) REVERT: W 83 ASP cc_start: 0.8097 (t0) cc_final: 0.7815 (t0) REVERT: W 93 LEU cc_start: 0.9352 (tt) cc_final: 0.9052 (tt) REVERT: W 95 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8187 (mt-10) REVERT: W 109 PHE cc_start: 0.8843 (m-80) cc_final: 0.8589 (m-80) REVERT: X 111 VAL cc_start: 0.8534 (p) cc_final: 0.8286 (m) REVERT: Z 50 MET cc_start: 0.8267 (tpp) cc_final: 0.8059 (tpp) REVERT: Z 76 GLN cc_start: 0.8841 (tp40) cc_final: 0.8557 (tp40) REVERT: a 53 ARG cc_start: 0.8510 (mtm110) cc_final: 0.8006 (ttt-90) REVERT: a 60 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8120 (p90) REVERT: b 8 PHE cc_start: 0.7406 (t80) cc_final: 0.6991 (t80) REVERT: b 15 LYS cc_start: 0.9020 (pttp) cc_final: 0.8694 (mmtt) REVERT: b 32 MET cc_start: 0.8269 (mmm) cc_final: 0.7769 (tpt) REVERT: b 51 TYR cc_start: 0.8128 (m-80) cc_final: 0.7058 (t80) REVERT: q 58 ARG cc_start: 0.6413 (ttt180) cc_final: 0.6185 (ttt180) REVERT: q 77 VAL cc_start: 0.8220 (t) cc_final: 0.7970 (p) REVERT: q 93 MET cc_start: 0.8051 (mtp) cc_final: 0.7721 (mtp) REVERT: q 132 LYS cc_start: 0.7280 (tmmt) cc_final: 0.6795 (tmmt) outliers start: 108 outliers final: 77 residues processed: 883 average time/residue: 0.1984 time to fit residues: 289.9046 Evaluate side-chains 876 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 784 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 377 GLU 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 228 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 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 640 ASP 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 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 215 TYR 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 103 LEU Chi-restraints excluded: chain I residue 129 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 259 VAL 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 R residue 46 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 93 ILE 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 84 LEU Chi-restraints excluded: chain T residue 123 GLU Chi-restraints excluded: chain T residue 124 ASP Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 123 SER Chi-restraints excluded: chain X residue 22 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 Z residue 78 GLU Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain a residue 60 TYR Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 66 VAL 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 r residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 131 optimal weight: 0.0970 chunk 288 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 404 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 269 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 106 HIS ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 178 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 ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN P 79 GLN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 ASN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 ASN s 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.105203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084032 restraints weight = 103617.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.085115 restraints weight = 45424.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.086320 restraints weight = 32525.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086266 restraints weight = 26703.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.086744 restraints weight = 25405.850| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 34767 Z= 0.152 Angle : 0.980 81.111 47131 Z= 0.382 Chirality : 0.047 0.391 5134 Planarity : 0.005 0.129 5962 Dihedral : 8.518 129.214 4952 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 2.85 % Allowed : 26.53 % Favored : 70.63 % 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: -0.25 (0.13), residues: 4121 helix: 0.74 (0.12), residues: 1888 sheet: -0.95 (0.27), residues: 367 loop : -0.87 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG r 27 TYR 0.040 0.002 TYR b 53 PHE 0.030 0.002 PHE q 74 TRP 0.081 0.002 TRP b 26 HIS 0.011 0.001 HIS X 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (34726) covalent geometry : angle 0.76226 / 0.38 (47039) SS BOND : bond 0.00167 / 0.09 ( 4) SS BOND : angle 0.35110 / 0.18 ( 8) hydrogen bonds : bond 0.04085 / 2.67 ( 1411) hydrogen bonds : angle 5.06073 / 3.62 ( 4116) metal coordination : bond 0.01524 / 0.94 ( 37) metal coordination : angle 14.60359 / 10.72 ( 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 923 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 820 time to evaluate : 1.156 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: A 53 MET cc_start: 0.8309 (mpp) cc_final: 0.7608 (tpp) REVERT: B 77 LYS cc_start: 0.9038 (mttt) cc_final: 0.8651 (mttm) REVERT: B 107 MET cc_start: 0.8541 (tpt) cc_final: 0.8079 (tpt) REVERT: B 131 MET cc_start: 0.8440 (ttm) cc_final: 0.7801 (ttt) REVERT: B 147 LYS cc_start: 0.8784 (mttt) cc_final: 0.8189 (ttpt) REVERT: B 176 SER cc_start: 0.9190 (m) cc_final: 0.8990 (t) REVERT: B 220 ILE cc_start: 0.9149 (tp) cc_final: 0.8897 (tp) REVERT: C 117 ASP cc_start: 0.8425 (t0) cc_final: 0.8181 (t0) REVERT: C 149 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9256 (pp) REVERT: C 207 VAL cc_start: 0.9596 (m) cc_final: 0.9370 (p) REVERT: D 80 MET cc_start: 0.7208 (mmp) cc_final: 0.6704 (ttp) REVERT: D 205 GLU cc_start: 0.7932 (tp30) cc_final: 0.7346 (tp30) REVERT: D 292 MET cc_start: 0.8729 (mmm) cc_final: 0.8413 (mmt) REVERT: D 294 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7569 (mtm-85) REVERT: E 59 TYR cc_start: 0.8833 (m-80) cc_final: 0.8299 (m-80) REVERT: E 97 MET cc_start: 0.8360 (mtm) cc_final: 0.8150 (mtm) REVERT: E 105 GLN cc_start: 0.8960 (pt0) cc_final: 0.8719 (pm20) REVERT: E 113 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7624 (mt-10) REVERT: E 123 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7232 (mtp180) REVERT: E 124 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7521 (ttpt) REVERT: E 145 ASP cc_start: 0.9076 (t0) cc_final: 0.8600 (m-30) REVERT: E 181 ASN cc_start: 0.7580 (t0) cc_final: 0.7130 (t0) REVERT: F 168 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7730 (t0) REVERT: F 209 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8165 (mp0) REVERT: F 217 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8219 (tm-30) REVERT: F 276 PHE cc_start: 0.6670 (m-10) cc_final: 0.6429 (m-10) REVERT: F 386 ARG cc_start: 0.9064 (ttm110) cc_final: 0.8641 (ttp-110) REVERT: F 394 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8372 (mmtt) REVERT: G 42 MET cc_start: 0.9292 (mmm) cc_final: 0.9085 (mmm) REVERT: G 74 ASN cc_start: 0.8750 (t0) cc_final: 0.8516 (t0) REVERT: G 77 MET cc_start: 0.8862 (tpp) cc_final: 0.8623 (tpp) REVERT: G 94 MET cc_start: 0.8696 (tpt) cc_final: 0.8356 (tpp) REVERT: G 138 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8055 (t0) REVERT: G 264 SER cc_start: 0.9331 (m) cc_final: 0.8852 (p) REVERT: G 306 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8022 (mtm) REVERT: G 396 GLU cc_start: 0.8178 (tt0) cc_final: 0.7822 (tp30) REVERT: G 579 MET cc_start: 0.8313 (ptt) cc_final: 0.7812 (ppp) REVERT: G 605 GLN cc_start: 0.8085 (pp30) cc_final: 0.7835 (pp30) REVERT: G 608 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8510 (m) REVERT: G 618 GLU cc_start: 0.8656 (mp0) cc_final: 0.8266 (mp0) REVERT: G 628 GLU cc_start: 0.8539 (tt0) cc_final: 0.8307 (tt0) REVERT: G 707 MET cc_start: 0.9333 (mmm) cc_final: 0.9106 (mmm) REVERT: H 15 ILE cc_start: 0.9277 (mm) cc_final: 0.9035 (mt) REVERT: H 58 LYS cc_start: 0.8781 (tppp) cc_final: 0.8278 (tppt) REVERT: H 80 THR cc_start: 0.9588 (t) cc_final: 0.9316 (p) REVERT: H 134 ARG cc_start: 0.8846 (mtm180) cc_final: 0.8567 (mtm180) REVERT: H 173 TRP cc_start: 0.8202 (m-10) cc_final: 0.7596 (m-90) REVERT: H 183 MET cc_start: 0.9095 (mtt) cc_final: 0.8526 (mtt) REVERT: H 184 MET cc_start: 0.8909 (mmt) cc_final: 0.8469 (mmt) REVERT: H 224 PHE cc_start: 0.8563 (t80) cc_final: 0.8059 (t80) REVERT: H 234 MET cc_start: 0.9134 (mmm) cc_final: 0.8785 (mmm) REVERT: H 247 TYR cc_start: 0.8078 (t80) cc_final: 0.7756 (t80) REVERT: H 253 GLU cc_start: 0.8009 (pm20) cc_final: 0.6765 (tt0) REVERT: H 282 TYR cc_start: 0.7652 (t80) cc_final: 0.6996 (t80) REVERT: H 286 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8319 (mpp) REVERT: I 55 ASP cc_start: 0.8232 (m-30) cc_final: 0.7657 (t70) REVERT: I 76 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7704 (t80) REVERT: I 94 SER cc_start: 0.8807 (p) cc_final: 0.8484 (p) REVERT: I 117 LYS cc_start: 0.9249 (mtmt) cc_final: 0.9013 (mtpp) REVERT: I 133 GLU cc_start: 0.8111 (tt0) cc_final: 0.7754 (tm-30) REVERT: I 191 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8588 (tt) REVERT: I 208 ASP cc_start: 0.8422 (t0) cc_final: 0.7978 (t70) REVERT: P 97 MET cc_start: 0.7934 (ptp) cc_final: 0.7656 (ptp) REVERT: P 210 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7413 (tp30) REVERT: P 283 MET cc_start: 0.7807 (mmp) cc_final: 0.6537 (tpp) REVERT: P 298 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7059 (t80) REVERT: P 328 MET cc_start: 0.7554 (mmm) cc_final: 0.7304 (mmm) REVERT: Q 96 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8278 (mttp) REVERT: Q 99 MET cc_start: 0.9121 (ptp) cc_final: 0.8845 (ptp) REVERT: Q 128 PHE cc_start: 0.8678 (m-80) cc_final: 0.8410 (m-80) REVERT: Q 164 PHE cc_start: 0.8534 (m-10) cc_final: 0.8185 (m-10) REVERT: Q 165 SER cc_start: 0.8603 (m) cc_final: 0.8343 (p) REVERT: R 45 ARG cc_start: 0.2582 (ptt180) cc_final: 0.2117 (tmm-80) REVERT: R 73 GLU cc_start: 0.8364 (pm20) cc_final: 0.8017 (pm20) REVERT: R 80 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7747 (t0) REVERT: S 40 ARG cc_start: 0.9171 (mtt180) cc_final: 0.8597 (mtm180) REVERT: S 45 LYS cc_start: 0.9132 (tptt) cc_final: 0.8740 (mmmt) REVERT: T 80 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8710 (tptt) REVERT: T 88 LYS cc_start: 0.8367 (tptt) cc_final: 0.7866 (mmmt) REVERT: T 129 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7546 (tp30) REVERT: T 130 ILE cc_start: 0.8011 (mm) cc_final: 0.7544 (mm) REVERT: V 53 ASN cc_start: 0.8786 (m-40) cc_final: 0.8378 (m-40) REVERT: W 24 PHE cc_start: 0.8718 (m-80) cc_final: 0.8271 (m-80) REVERT: W 45 GLU cc_start: 0.8530 (tp30) cc_final: 0.7959 (tp30) REVERT: W 54 GLN cc_start: 0.9040 (mt0) cc_final: 0.8478 (mp10) REVERT: W 61 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8642 (mm-40) REVERT: W 93 LEU cc_start: 0.9325 (tt) cc_final: 0.9026 (tt) REVERT: W 95 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8152 (mt-10) REVERT: W 109 PHE cc_start: 0.8808 (m-80) cc_final: 0.8598 (m-80) REVERT: X 44 MET cc_start: 0.8750 (tpp) cc_final: 0.8531 (mtt) REVERT: X 111 VAL cc_start: 0.8561 (p) cc_final: 0.8317 (m) REVERT: Z 50 MET cc_start: 0.8201 (tpp) cc_final: 0.7956 (tpp) REVERT: Z 76 GLN cc_start: 0.8906 (tp40) cc_final: 0.8588 (tp40) REVERT: a 53 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8002 (ttt-90) REVERT: a 60 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8112 (p90) REVERT: b 8 PHE cc_start: 0.7393 (t80) cc_final: 0.7042 (t80) REVERT: b 15 LYS cc_start: 0.9044 (pttp) cc_final: 0.8718 (mmtt) REVERT: b 32 MET cc_start: 0.8242 (mmm) cc_final: 0.7742 (tpt) REVERT: b 51 TYR cc_start: 0.8065 (m-80) cc_final: 0.7164 (t80) REVERT: b 53 TYR cc_start: 0.8168 (t80) cc_final: 0.7943 (t80) REVERT: q 93 MET cc_start: 0.8126 (mtp) cc_final: 0.7833 (mtp) REVERT: q 132 LYS cc_start: 0.7445 (tmmt) cc_final: 0.6914 (tmmt) outliers start: 103 outliers final: 76 residues processed: 879 average time/residue: 0.1943 time to fit residues: 282.4369 Evaluate side-chains 878 residues out of total 3619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 788 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 113 TRP Chi-restraints excluded: chain B residue 83 ASN 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 120 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain F residue 168 ASN Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 377 GLU 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 228 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 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 640 ASP 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 153 VAL 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 215 TYR 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 103 LEU Chi-restraints excluded: chain I residue 129 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 259 VAL 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 166 TRP Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 93 ILE 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 84 LEU Chi-restraints excluded: chain T residue 123 GLU Chi-restraints excluded: chain T residue 124 ASP Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 76 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 128 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 78 GLU Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 38 VAL 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 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 r residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 231 optimal weight: 0.7980 chunk 345 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 316 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 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** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.106099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085429 restraints weight = 102853.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086207 restraints weight = 45911.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.087382 restraints weight = 34115.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087576 restraints weight = 27843.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088033 restraints weight = 25959.304| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.7311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 34767 Z= 0.150 Angle : 0.975 81.381 47131 Z= 0.380 Chirality : 0.047 0.358 5134 Planarity : 0.005 0.129 5962 Dihedral : 8.438 128.293 4952 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 2.65 % Allowed : 27.16 % 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: -0.25 (0.13), residues: 4121 helix: 0.73 (0.12), residues: 1885 sheet: -0.96 (0.27), residues: 365 loop : -0.86 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG q 58 TYR 0.036 0.002 TYR I 86 PHE 0.028 0.002 PHE q 74 TRP 0.100 0.003 TRP a 45 HIS 0.010 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (34726) covalent geometry : angle 0.76036 / 0.38 (47039) SS BOND : bond 0.00164 / 0.09 ( 4) SS BOND : angle 0.34097 / 0.16 ( 8) hydrogen bonds : bond 0.04060 / 2.67 ( 1411) hydrogen bonds : angle 5.05260 / 3.61 ( 4116) metal coordination : bond 0.01474 / 0.91 ( 37) metal coordination : angle 14.47861 / 10.65 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7624.65 seconds wall clock time: 132 minutes 4.11 seconds (7924.11 seconds total)