Starting phenix.real_space_refine on Sun Aug 9 08:25:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnv_38516/08_2026/8xnv_38516_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnv_38516/08_2026/8xnv_38516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnv_38516/08_2026/8xnv_38516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnv_38516/08_2026/8xnv_38516.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnv_38516/08_2026/8xnv_38516_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnv_38516/08_2026/8xnv_38516_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 12 5.49 5 S 245 5.16 5 C 21933 2.51 5 N 5815 2.21 5 O 6217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34251 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 2 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 10, 'TRANS': 144} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1643 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: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2525 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 22, 'TRANS': 293} Chain breaks: 1 Chain: "I" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1380 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain breaks: 1 Chain: "P" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2720 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 940 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} 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: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1145 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "q" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1025 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain breaks: 1 Chain: "r" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 10, 'TRANS': 73} Chain breaks: 2 Chain: "s" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 193 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UQ1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'3PE': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 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: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "a" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1045 SG CYS B 99 82.046 60.075 105.451 1.00 29.52 S ATOM 1051 SG CYS B 100 80.959 56.333 103.915 1.00 30.11 S ATOM 1548 SG CYS B 164 77.890 56.265 107.751 1.00 28.96 S ATOM 1778 SG CYS B 194 84.004 56.688 108.529 1.00 29.28 S ATOM 7560 SG CYS E 134 141.471 52.274 151.483 1.00 56.01 S ATOM 7594 SG CYS E 139 144.296 53.988 150.502 1.00 56.50 S ATOM 7878 SG CYS E 175 139.252 55.986 153.907 1.00 54.42 S ATOM 7901 SG CYS E 179 142.501 57.836 153.581 1.00 57.95 S ATOM 11431 SG CYS F 425 123.001 61.855 153.933 1.00 45.60 S ATOM 11109 SG CYS F 385 123.011 59.233 148.205 1.00 39.95 S ATOM 11089 SG CYS F 382 118.756 60.496 150.441 1.00 40.29 S ATOM 11070 SG CYS F 379 120.676 56.485 153.407 1.00 43.09 S ATOM 12479 SG CYS G 131 102.542 49.118 137.140 1.00 31.31 S ATOM 12458 SG CYS G 128 104.599 52.814 132.446 1.00 30.26 S ATOM 12519 SG CYS G 137 102.265 55.062 138.405 1.00 33.13 S ATOM 13204 SG CYS G 226 104.060 49.341 145.730 1.00 34.31 S ATOM 12875 SG CYS G 182 107.101 48.054 150.999 1.00 36.31 S ATOM 12851 SG CYS G 179 106.619 53.303 148.840 1.00 35.62 S ATOM 12828 SG CYS G 176 110.022 48.938 146.492 1.00 34.05 S ATOM 11965 SG CYS G 64 108.083 59.380 150.695 1.00 35.53 S ATOM 12051 SG CYS G 75 108.835 61.370 148.978 1.00 36.47 S ATOM 12076 SG CYS G 78 107.750 66.001 150.995 1.00 36.76 S ATOM 12177 SG CYS G 92 105.267 64.008 152.987 1.00 39.04 S ATOM 20400 SG CYS I 152 88.165 50.528 113.067 1.00 27.39 S ATOM 20174 SG CYS I 123 87.817 51.830 118.388 1.00 27.30 S ATOM 20426 SG CYS I 155 90.675 55.363 114.512 1.00 27.04 S ATOM 20447 SG CYS I 158 93.697 50.123 115.568 1.00 26.60 S ATOM 20146 SG CYS I 119 93.903 47.645 122.124 1.00 28.85 S ATOM 20476 SG CYS I 162 100.157 47.221 120.009 1.00 28.07 S ATOM 20104 SG CYS I 113 96.638 42.478 122.506 1.00 28.61 S ATOM 20123 SG CYS I 116 99.184 46.918 126.006 1.00 29.24 S ATOM 24958 SG CYS R 79 113.162 40.446 125.161 1.00 32.60 S ATOM 25134 SG CYS R 104 110.697 39.160 126.652 1.00 32.49 S ATOM 25156 SG CYS R 107 110.044 39.730 123.208 1.00 30.78 S Time building chain proxies: 6.16, per 1000 atoms: 0.18 Number of scatterers: 34251 At special positions: 0 Unit cell: (169.4, 128.7, 201.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 245 16.00 P 12 15.00 O 6217 8.00 N 5815 7.00 C 21933 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=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.04 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 898.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 164 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " 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="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " 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=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE1 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 116 " 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 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7902 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 34 sheets defined 48.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 removed outlier: 3.508A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 71 removed outlier: 3.579A pdb=" N PHE A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 83 through 109 Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 4.095A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 removed outlier: 3.911A pdb=" N ASP B 113 " --> pdb=" O PRO B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 180 through 185 removed outlier: 4.228A pdb=" N ILE B 184 " --> pdb=" O GLY B 180 " (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: 3.960A 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 155 through 158 Processing helix chain 'C' and resid 159 through 160 No H-bonds generated for 'chain 'C' and resid 159 through 160' Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.034A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.924A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.737A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 138' Processing helix chain 'D' and resid 143 through 159 removed outlier: 4.134A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 216 removed outlier: 3.829A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 4.088A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.750A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.525A pdb=" N LYS D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 434 Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.677A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.834A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.609A pdb=" N ASN E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.613A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'F' and resid 36 through 40 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: 4.296A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 removed outlier: 4.184A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 4.032A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.636A pdb=" N GLY F 188 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 4.260A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 257 removed outlier: 3.588A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing helix chain 'F' and resid 258 through 266 removed outlier: 4.016A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.860A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.732A 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: 3.547A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.662A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.723A 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: 3.519A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.599A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.774A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.728A 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 147 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 200 through 204 Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.821A 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 361 Processing helix chain 'G' and resid 377 through 386 removed outlier: 4.303A pdb=" N LEU G 381 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG G 382 " --> pdb=" O THR G 379 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER G 383 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.588A 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: 4.009A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.677A 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 529 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 556 through 560 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 665 through 675 Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.642A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.352A 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 2 through 32 removed outlier: 3.604A pdb=" N VAL H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 4.398A pdb=" N ALA H 16 " --> pdb=" O PRO H 12 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG H 25 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 removed outlier: 3.901A pdb=" N ALA H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.704A pdb=" N LEU H 79 " --> pdb=" O PRO H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 123 removed outlier: 3.673A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 158 removed outlier: 3.518A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 169 removed outlier: 3.674A pdb=" N LEU H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 191 Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.803A pdb=" N GLU H 214 " --> pdb=" O PHE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 226 removed outlier: 3.585A pdb=" N PHE H 220 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 Processing helix chain 'H' and resid 237 through 242 Processing helix chain 'H' and resid 252 through 275 removed outlier: 4.396A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU H 265 " --> pdb=" O MET H 261 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE H 273 " --> pdb=" O THR H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 292 removed outlier: 3.607A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 312 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 58 Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.770A pdb=" N MET I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 187 through 195 removed outlier: 3.584A pdb=" N ASN I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN I 193 " --> pdb=" O LYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 209 removed outlier: 4.284A pdb=" N ALA I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN I 204 " --> pdb=" O GLU I 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 76 Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.589A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 91 through 96' Processing helix chain 'P' and resid 114 through 122 removed outlier: 4.505A 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 Processing helix chain 'P' and resid 213 through 220 Processing helix chain 'P' and resid 228 through 233 removed outlier: 3.773A pdb=" N LEU P 231 " --> pdb=" O LEU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 255 through 259 Processing helix chain 'P' and resid 273 through 284 removed outlier: 4.118A pdb=" N GLY P 282 " --> pdb=" O LYS P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.937A pdb=" N LEU P 304 " --> pdb=" O TRP P 300 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE P 305 " --> pdb=" O ILE P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 Processing helix chain 'P' and resid 334 through 339 Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.445A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 72 Processing helix chain 'Q' and resid 130 through 142 removed outlier: 3.520A pdb=" N PHE Q 137 " --> pdb=" O ASP Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 165 Processing helix chain 'R' and resid 42 through 49 removed outlier: 4.167A pdb=" N ARG R 47 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'S' and resid 32 through 48 removed outlier: 6.311A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS S 46 " --> pdb=" O VAL S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 Processing helix chain 'T' and resid 111 through 127 removed outlier: 3.591A pdb=" N VAL T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU T 117 " --> pdb=" O LEU T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 138 Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 35 Processing helix chain 'V' and resid 36 through 38 No H-bonds generated for 'chain 'V' and resid 36 through 38' Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.708A pdb=" N GLN V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU V 54 " --> pdb=" O GLN V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 73 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.681A pdb=" N LYS V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.991A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 Processing helix chain 'W' and resid 78 through 98 removed outlier: 3.948A pdb=" N ILE W 87 " --> pdb=" O ASP W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 108 Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'X' and resid 9 through 14 Processing helix chain 'X' and resid 21 through 28 removed outlier: 3.544A pdb=" N LEU X 25 " --> pdb=" O SER X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 35 Processing helix chain 'X' and resid 37 through 50 removed outlier: 3.680A pdb=" N GLU X 42 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE X 43 " --> pdb=" O THR X 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU X 49 " --> pdb=" O LEU X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 77 removed outlier: 4.055A pdb=" N LEU X 68 " --> pdb=" O ASN X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.894A pdb=" N CYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 removed outlier: 3.900A pdb=" N ALA X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS X 110 " --> pdb=" O LYS X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 144 Processing helix chain 'Z' and resid 31 through 87 removed outlier: 3.544A pdb=" N GLY Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG Z 68 " --> pdb=" O ASP Z 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Proline residue: Z 73 - end of helix removed outlier: 3.660A pdb=" N LEU Z 87 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 96 removed outlier: 3.716A pdb=" N GLU Z 93 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 138 Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 17 through 27 Processing helix chain 'a' and resid 41 through 55 removed outlier: 3.739A pdb=" N TRP a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 4.032A pdb=" N ASN b 11 " --> pdb=" O ALA b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 23 Processing helix chain 'b' and resid 24 through 35 removed outlier: 3.581A pdb=" N ALA b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE b 30 " --> pdb=" O TRP b 26 " (cutoff:3.500A) Proline residue: b 33 - end of helix Processing helix chain 'b' and resid 38 through 40 No H-bonds generated for 'chain 'b' and resid 38 through 40' Processing helix chain 'b' and resid 41 through 49 removed outlier: 3.533A pdb=" N ASN b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS b 47 " --> pdb=" O SER b 43 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.740A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS q 8 " --> pdb=" O VAL q 4 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 28 Processing helix chain 'q' and resid 43 through 45 No H-bonds generated for 'chain 'q' and resid 43 through 45' Processing helix chain 'q' and resid 78 through 82 removed outlier: 4.201A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 3.983A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 17 Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.723A pdb=" N VAL r 63 " --> pdb=" O GLY r 59 " (cutoff:3.500A) Processing helix chain 's' and resid 78 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 96 removed outlier: 3.573A pdb=" N ILE B 189 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.858A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C 83 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.399A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.558A pdb=" N MET D 80 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET D 105 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N HIS D 442 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 394 through 401 Processing sheet with id=AA7, first strand: chain 'E' and resid 168 through 171 removed outlier: 6.566A pdb=" N TYR E 129 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE E 171 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 131 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.440A 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: 6.231A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.752A 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: 3.576A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AA9, 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: 7.485A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.599A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB3, first strand: chain 'G' and resid 35 through 36 removed outlier: 6.776A pdb=" N PHE G 35 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB5, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AB6, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.350A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 306 through 309 Processing sheet with id=AB8, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.096A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N CYS G 367 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA G 340 " --> pdb=" O CYS G 367 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.322A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASN G 514 " --> pdb=" O PRO G 472 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL G 474 " --> pdb=" O ASN G 514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'I' and resid 132 through 134 removed outlier: 3.573A pdb=" N ARG I 141 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 146 through 148 Processing sheet with id=AC5, first strand: chain 'P' and resid 56 through 58 removed outlier: 5.863A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE P 201 " --> pdb=" O PHE P 164 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N HIS P 166 " --> pdb=" O ILE P 201 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE P 200 " --> pdb=" O PHE P 263 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE P 265 " --> pdb=" O ILE P 200 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG P 202 " --> pdb=" O PHE P 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 80 through 84 removed outlier: 3.848A pdb=" N LEU P 106 " --> pdb=" O ILE P 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 205 through 207 removed outlier: 6.368A pdb=" N ASP P 205 " --> pdb=" O VAL P 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'P' and resid 236 through 237 Processing sheet with id=AC9, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'Q' and resid 78 through 80 removed outlier: 4.055A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU Q 126 " --> pdb=" O MET Q 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD3, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD4, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.507A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 55 through 57 Processing sheet with id=AD6, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'q' and resid 37 through 41 removed outlier: 3.825A pdb=" N THR q 37 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR q 48 " --> pdb=" O VAL q 39 " (cutoff:3.500A) 1334 hydrogen bonds defined for protein. 3777 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: 5.69 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 13578 1.38 - 1.59: 21031 1.59 - 1.81: 318 1.81 - 2.02: 65 2.02 - 2.23: 80 Bond restraints: 35072 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.646 0.732 2.00e-02 2.50e+03 1.34e+03 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.398 -0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C ARG Q 106 " pdb=" O ARG Q 106 " ideal model delta sigma weight residual 1.236 1.339 -0.103 1.14e-02 7.69e+03 8.17e+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 7.62e+01 bond pdb=" CA TYR Z 143 " pdb=" C TYR Z 143 " ideal model delta sigma weight residual 1.524 1.420 0.103 1.23e-02 6.61e+03 7.06e+01 ... (remaining 35067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.45: 46760 6.45 - 12.89: 582 12.89 - 19.34: 173 19.34 - 25.79: 7 25.79 - 32.24: 2 Bond angle restraints: 47524 Sorted by residual: angle pdb=" N ILE H 231 " pdb=" CA ILE H 231 " pdb=" C ILE H 231 " ideal model delta sigma weight residual 113.42 90.97 22.45 1.17e+00 7.31e-01 3.68e+02 angle pdb=" N TYR B 170 " pdb=" CA TYR B 170 " pdb=" C TYR B 170 " ideal model delta sigma weight residual 111.33 90.07 21.26 1.21e+00 6.83e-01 3.09e+02 angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.00 25.64 1.52e+00 4.33e-01 2.85e+02 angle pdb=" N CYS F 125 " pdb=" CA CYS F 125 " pdb=" C CYS F 125 " ideal model delta sigma weight residual 113.17 93.47 19.70 1.26e+00 6.30e-01 2.45e+02 angle pdb=" N CYS B 99 " pdb=" CA CYS B 99 " pdb=" C CYS B 99 " ideal model delta sigma weight residual 114.31 94.47 19.84 1.29e+00 6.01e-01 2.37e+02 ... (remaining 47519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.05: 20420 26.05 - 52.10: 693 52.10 - 78.15: 64 78.15 - 104.20: 23 104.20 - 130.25: 7 Dihedral angle restraints: 21207 sinusoidal: 8951 harmonic: 12256 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 171.64 -78.64 1 1.00e+01 1.00e-02 7.71e+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 93.00 154.25 -61.25 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" N THR I 64 " pdb=" C THR I 64 " pdb=" CA THR I 64 " pdb=" CB THR I 64 " ideal model delta harmonic sigma weight residual 123.40 106.29 17.11 0 2.50e+00 1.60e-01 4.68e+01 ... (remaining 21204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4734 0.190 - 0.380: 406 0.380 - 0.570: 24 0.570 - 0.760: 3 0.760 - 0.950: 24 Chirality restraints: 5191 Sorted by residual: chirality pdb="FE3 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.61 -0.95 2.00e-01 2.50e+01 2.25e+01 chirality pdb="FE1 SF4 I 303 " pdb=" S2 SF4 I 303 " pdb=" S3 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False -10.55 -9.63 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb="FE2 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S3 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False 10.55 9.64 0.92 2.00e-01 2.50e+01 2.10e+01 ... (remaining 5188 not shown) Planarity restraints: 6032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 UQ9 H 400 " 0.272 2.00e-02 2.50e+03 2.31e-01 6.69e+02 pdb=" C13 UQ9 H 400 " -0.392 2.00e-02 2.50e+03 pdb=" C14 UQ9 H 400 " -0.085 2.00e-02 2.50e+03 pdb=" C15 UQ9 H 400 " 0.025 2.00e-02 2.50e+03 pdb=" C16 UQ9 H 400 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 400 " 0.032 2.00e-02 2.50e+03 1.31e-01 5.16e+02 pdb=" C1M UQ9 H 400 " 0.187 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 400 " -0.020 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 400 " 0.002 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 400 " -0.024 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 400 " 0.067 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 400 " -0.066 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 400 " -0.262 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 400 " -0.075 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 400 " 0.051 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 400 " -0.144 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 400 " 0.251 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 H 400 " 0.021 2.00e-02 2.50e+03 1.68e-01 3.54e+02 pdb=" C11 UQ9 H 400 " -0.152 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 400 " -0.203 2.00e-02 2.50e+03 pdb=" C8 UQ9 H 400 " 0.269 2.00e-02 2.50e+03 pdb=" C9 UQ9 H 400 " 0.065 2.00e-02 2.50e+03 ... (remaining 6029 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 428 2.53 - 3.12: 31104 3.12 - 3.72: 54603 3.72 - 4.31: 82632 4.31 - 4.90: 131021 Nonbonded interactions: 299788 Sorted by model distance: nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.942 3.040 nonbonded pdb=" OD1 ASP C 147 " pdb=" OE1 GLU C 148 " model vdw 1.999 3.040 nonbonded pdb=" O PHE G 63 " pdb=" SG CYS G 64 " model vdw 2.007 3.400 nonbonded pdb=" O ASN Z 24 " pdb=" OD1 ASN Z 24 " model vdw 2.046 3.040 nonbonded pdb=" N THR G 174 " pdb=" N ARG G 175 " model vdw 2.079 2.560 ... (remaining 299783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.880 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.241 35113 Z= 1.019 Angle : 2.197 56.971 47616 Z= 1.433 Chirality : 0.122 0.950 5191 Planarity : 0.009 0.231 6032 Dihedral : 13.058 130.252 13293 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 45.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.44 % Rotamer: Outliers : 0.49 % Allowed : 7.37 % Favored : 92.14 % Cbeta Deviations : 1.09 % 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: -3.31 (0.11), residues: 4166 helix: -1.85 (0.11), residues: 1761 sheet: -2.15 (0.27), residues: 328 loop : -2.51 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 68 TYR 0.067 0.003 TYR D 135 PHE 0.031 0.002 PHE I 175 TRP 0.033 0.002 TRP G 285 HIS 0.011 0.002 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.01477 / 0.92 (35072) covalent geometry : angle 2.07741 / 1.43 (47524) SS BOND : bond 0.00898 / 0.45 ( 4) SS BOND : angle 1.30879 / 0.64 ( 8) hydrogen bonds : bond 0.25045 / 16.38 ( 1334) hydrogen bonds : angle 9.67123 / 6.86 ( 3777) metal coordination : bond 0.49244 / 31.69 ( 37) metal coordination : angle 17.12976 / 12.68 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1525 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 1507 time to evaluate : 1.292 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: C 103 THR cc_start: 0.9012 (m) cc_final: 0.8740 (m) REVERT: C 137 ASN cc_start: 0.8444 (t0) cc_final: 0.8225 (t0) REVERT: C 188 THR cc_start: 0.8807 (p) cc_final: 0.8512 (p) REVERT: D 140 ASP cc_start: 0.7807 (t0) cc_final: 0.7352 (t0) REVERT: D 160 ASN cc_start: 0.8019 (t0) cc_final: 0.7803 (t0) REVERT: D 185 MET cc_start: 0.8529 (tpt) cc_final: 0.7980 (tpt) REVERT: D 215 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7164 (tt0) REVERT: D 389 TYR cc_start: 0.7575 (m-10) cc_final: 0.7313 (m-10) REVERT: E 167 LEU cc_start: 0.7072 (tp) cc_final: 0.6637 (tp) REVERT: E 205 ASP cc_start: 0.7631 (m-30) cc_final: 0.7001 (m-30) REVERT: F 300 ILE cc_start: 0.6726 (mt) cc_final: 0.6467 (mt) REVERT: F 337 MET cc_start: 0.7313 (mmp) cc_final: 0.7101 (mmp) REVERT: G 213 MET cc_start: 0.8263 (ptm) cc_final: 0.7525 (ptp) REVERT: G 294 TYR cc_start: 0.7879 (p90) cc_final: 0.7427 (p90) REVERT: G 620 TRP cc_start: 0.8450 (p-90) cc_final: 0.8126 (p-90) REVERT: H 90 PRO cc_start: 0.7904 (Cg_endo) cc_final: 0.7531 (Cg_exo) REVERT: H 93 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.7235 (m170) REVERT: H 215 TYR cc_start: 0.7847 (m-80) cc_final: 0.7558 (m-80) REVERT: I 89 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6561 (mt-10) REVERT: I 145 TYR cc_start: 0.8040 (t80) cc_final: 0.7628 (t80) REVERT: P 84 TYR cc_start: 0.8782 (p90) cc_final: 0.8510 (p90) REVERT: P 134 TRP cc_start: 0.7707 (p90) cc_final: 0.7160 (p90) REVERT: R 64 ILE cc_start: 0.6194 (tp) cc_final: 0.5553 (tp) REVERT: S 53 ILE cc_start: 0.9051 (mt) cc_final: 0.8720 (mt) REVERT: S 65 LEU cc_start: 0.8813 (tt) cc_final: 0.8485 (tt) REVERT: T 126 PHE cc_start: 0.7578 (m-80) cc_final: 0.7068 (m-80) REVERT: V 64 ASP cc_start: 0.6847 (t0) cc_final: 0.6042 (t0) REVERT: W 43 TYR cc_start: 0.8544 (t80) cc_final: 0.7521 (t80) REVERT: W 63 ARG cc_start: 0.8396 (mtt180) cc_final: 0.7977 (mtt180) REVERT: Z 76 GLN cc_start: 0.6874 (tp-100) cc_final: 0.6666 (tp-100) REVERT: a 47 LEU cc_start: 0.8979 (mp) cc_final: 0.8708 (mp) REVERT: q 124 TYR cc_start: 0.6735 (t80) cc_final: 0.6460 (t80) outliers start: 18 outliers final: 1 residues processed: 1516 average time/residue: 0.2290 time to fit residues: 548.2494 Evaluate side-chains 907 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 905 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 137 LYS Chi-restraints excluded: chain H residue 93 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN B 83 ASN B 106 HIS B 127 GLN B 151 GLN B 166 ASN B 209 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 130 ASN C 195 HIS ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS D 147 ASN D 149 GLN D 182 ASN D 234 GLN D 285 ASN D 313 GLN D 442 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 ASN E 245 GLN F 164 ASN F 436 GLN G 51 GLN G 74 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 ASN G 388 ASN G 495 ASN G 571 HIS G 572 HIS H 157 ASN H 171 HIS H 235 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 HIS ** I 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** P 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 ASN P 275 HIS Q 71 HIS Q 86 ASN Q 109 ASN ** S 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 142 GLN V 50 GLN W 48 ASN W 129 HIS ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 HIS Z 8 GLN Z 76 GLN a 31 ASN b 71 GLN q 17 HIS r 21 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.139379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.109198 restraints weight = 63778.051| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.77 r_work: 0.3343 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 35113 Z= 0.216 Angle : 1.046 63.617 47616 Z= 0.430 Chirality : 0.049 0.338 5191 Planarity : 0.007 0.078 6032 Dihedral : 10.282 162.533 4972 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.84 % Favored : 96.14 % Rotamer: Outliers : 3.00 % Allowed : 16.57 % Favored : 80.43 % 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: -1.87 (0.12), residues: 4166 helix: -0.52 (0.12), residues: 1827 sheet: -2.07 (0.25), residues: 363 loop : -1.73 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 88 TYR 0.021 0.002 TYR I 36 PHE 0.023 0.002 PHE W 121 TRP 0.028 0.002 TRP F 51 HIS 0.009 0.002 HIS R 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (35072) covalent geometry : angle 0.82335 / 0.43 (47524) SS BOND : bond 0.00350 / 0.18 ( 4) SS BOND : angle 2.68939 / 1.54 ( 8) hydrogen bonds : bond 0.05759 / 3.71 ( 1334) hydrogen bonds : angle 5.86940 / 4.20 ( 3777) metal coordination : bond 0.02493 / 1.63 ( 37) metal coordination : angle 15.37726 / 11.67 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 990 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9065 (tp) REVERT: B 82 ILE cc_start: 0.8796 (mm) cc_final: 0.8595 (mm) REVERT: B 83 ASN cc_start: 0.8277 (m-40) cc_final: 0.7988 (m-40) REVERT: B 145 LEU cc_start: 0.9360 (tp) cc_final: 0.9052 (tt) REVERT: C 76 GLN cc_start: 0.8699 (pt0) cc_final: 0.8010 (pm20) REVERT: C 168 GLU cc_start: 0.8362 (tt0) cc_final: 0.7988 (tt0) REVERT: C 211 TYR cc_start: 0.9205 (t80) cc_final: 0.8981 (t80) REVERT: D 95 LEU cc_start: 0.8833 (tp) cc_final: 0.8431 (tp) REVERT: D 97 LEU cc_start: 0.8751 (tp) cc_final: 0.8486 (tt) REVERT: D 110 ASP cc_start: 0.8270 (p0) cc_final: 0.7944 (p0) REVERT: D 285 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8269 (t0) REVERT: D 389 TYR cc_start: 0.8222 (m-10) cc_final: 0.7950 (m-10) REVERT: D 443 MET cc_start: 0.8951 (mtm) cc_final: 0.8673 (mtm) REVERT: E 40 HIS cc_start: 0.5376 (t-90) cc_final: 0.4546 (t-170) REVERT: E 129 TYR cc_start: 0.8822 (m-80) cc_final: 0.8614 (m-80) REVERT: E 161 GLU cc_start: 0.7402 (mp0) cc_final: 0.7158 (pm20) REVERT: E 165 ASP cc_start: 0.8320 (t70) cc_final: 0.7875 (p0) REVERT: E 189 ASP cc_start: 0.8380 (m-30) cc_final: 0.7250 (t0) REVERT: E 192 TYR cc_start: 0.7731 (m-80) cc_final: 0.7356 (m-80) REVERT: F 71 LYS cc_start: 0.8723 (mmpt) cc_final: 0.8232 (mttt) REVERT: F 75 TRP cc_start: 0.8208 (t60) cc_final: 0.7500 (t60) REVERT: F 93 PHE cc_start: 0.8374 (t80) cc_final: 0.8113 (t80) REVERT: F 118 ASP cc_start: 0.8045 (t70) cc_final: 0.7246 (t0) REVERT: F 170 GLN cc_start: 0.8828 (tt0) cc_final: 0.7922 (tm-30) REVERT: F 208 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7595 (tm-30) REVERT: F 255 CYS cc_start: 0.8657 (m) cc_final: 0.8224 (t) REVERT: F 291 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: G 118 GLU cc_start: 0.7970 (tt0) cc_final: 0.6983 (tt0) REVERT: G 152 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7848 (mtm-85) REVERT: G 172 ILE cc_start: 0.8973 (mt) cc_final: 0.8709 (mm) REVERT: G 197 THR cc_start: 0.8856 (p) cc_final: 0.8430 (p) REVERT: G 294 TYR cc_start: 0.8307 (p90) cc_final: 0.7674 (p90) REVERT: G 304 GLU cc_start: 0.8293 (tt0) cc_final: 0.8042 (tt0) REVERT: G 316 TYR cc_start: 0.8446 (m-80) cc_final: 0.7354 (m-80) REVERT: G 349 GLU cc_start: 0.8445 (mp0) cc_final: 0.8234 (mp0) REVERT: G 396 GLU cc_start: 0.8282 (tp30) cc_final: 0.8006 (tp30) REVERT: G 504 THR cc_start: 0.8622 (p) cc_final: 0.8278 (p) REVERT: G 530 TYR cc_start: 0.8723 (m-80) cc_final: 0.8224 (m-80) REVERT: G 652 ASN cc_start: 0.8720 (p0) cc_final: 0.8516 (p0) REVERT: H 87 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9017 (t) REVERT: H 130 PHE cc_start: 0.8054 (t80) cc_final: 0.7844 (t80) REVERT: H 215 TYR cc_start: 0.8588 (m-80) cc_final: 0.8121 (m-80) REVERT: H 318 MET cc_start: 0.7321 (mtm) cc_final: 0.6824 (tmm) REVERT: I 56 ASN cc_start: 0.8793 (t0) cc_final: 0.8338 (t0) REVERT: I 89 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7673 (mt-10) REVERT: P 84 TYR cc_start: 0.9199 (p90) cc_final: 0.8916 (p90) REVERT: P 177 SER cc_start: 0.8942 (t) cc_final: 0.8714 (p) REVERT: P 220 TYR cc_start: 0.7491 (m-10) cc_final: 0.7059 (m-10) REVERT: P 261 LYS cc_start: 0.7469 (mttt) cc_final: 0.7179 (tptp) REVERT: Q 108 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7211 (mm-30) REVERT: S 19 ILE cc_start: 0.9165 (mp) cc_final: 0.8894 (pt) REVERT: S 51 LEU cc_start: 0.8789 (tp) cc_final: 0.8576 (tt) REVERT: S 57 GLU cc_start: 0.7349 (tp30) cc_final: 0.7066 (tp30) REVERT: S 62 GLN cc_start: 0.8929 (pm20) cc_final: 0.8658 (pm20) REVERT: S 79 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7283 (pp) REVERT: T 80 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8597 (tptm) REVERT: T 90 TYR cc_start: 0.7984 (t80) cc_final: 0.6327 (t80) REVERT: T 104 PHE cc_start: 0.7563 (m-80) cc_final: 0.6893 (m-80) REVERT: T 107 ASP cc_start: 0.7480 (m-30) cc_final: 0.6416 (m-30) REVERT: T 110 LEU cc_start: 0.8457 (mt) cc_final: 0.8160 (mt) REVERT: T 111 ASP cc_start: 0.8243 (t0) cc_final: 0.7873 (t0) REVERT: T 114 ASP cc_start: 0.8454 (m-30) cc_final: 0.7439 (m-30) REVERT: T 126 PHE cc_start: 0.8016 (m-80) cc_final: 0.7321 (m-10) REVERT: T 128 PHE cc_start: 0.6652 (t80) cc_final: 0.6283 (t80) REVERT: T 134 ASP cc_start: 0.6045 (t0) cc_final: 0.5751 (t0) REVERT: V 67 LYS cc_start: 0.8811 (tptt) cc_final: 0.8575 (ttmt) REVERT: V 94 MET cc_start: 0.9041 (tpp) cc_final: 0.8804 (tpp) REVERT: W 27 ASP cc_start: 0.8013 (m-30) cc_final: 0.7644 (p0) REVERT: W 43 TYR cc_start: 0.8635 (t80) cc_final: 0.7878 (t80) REVERT: W 51 HIS cc_start: 0.8836 (t-90) cc_final: 0.8566 (t70) REVERT: W 54 GLN cc_start: 0.8642 (mt0) cc_final: 0.8190 (mm-40) REVERT: W 71 MET cc_start: 0.9174 (tpp) cc_final: 0.8835 (tpp) REVERT: X 44 MET cc_start: 0.8950 (mmt) cc_final: 0.8365 (mmt) REVERT: X 91 TYR cc_start: 0.8085 (t80) cc_final: 0.7096 (t80) REVERT: Z 82 ARG cc_start: 0.5223 (mtt-85) cc_final: 0.4974 (mtt-85) REVERT: a 25 TYR cc_start: 0.8119 (m-10) cc_final: 0.7903 (m-10) REVERT: a 30 THR cc_start: 0.8851 (m) cc_final: 0.8569 (p) REVERT: a 35 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7355 (mt-10) REVERT: b 16 GLU cc_start: 0.8276 (tp30) cc_final: 0.8017 (tp30) REVERT: q 85 GLU cc_start: 0.7450 (mp0) cc_final: 0.7240 (mp0) REVERT: q 124 TYR cc_start: 0.7438 (t80) cc_final: 0.6984 (t80) REVERT: q 132 LYS cc_start: 0.8104 (tmtt) cc_final: 0.7856 (tmtt) outliers start: 110 outliers final: 53 residues processed: 1049 average time/residue: 0.2020 time to fit residues: 347.3122 Evaluate side-chains 867 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 809 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 139 MET Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain q residue 31 ASN Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 45 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 396 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 363 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN D 381 HIS ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 281 HIS G 123 ASN G 140 GLN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN H 157 ASN H 235 ASN I 193 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 HIS S 22 HIS S 80 ASN T 103 HIS W 48 ASN W 73 ASN W 94 GLN ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 ASN a 58 ASN b 71 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.134793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104184 restraints weight = 64171.426| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.76 r_work: 0.3332 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 35113 Z= 0.220 Angle : 0.994 66.729 47616 Z= 0.391 Chirality : 0.047 0.356 5191 Planarity : 0.006 0.078 6032 Dihedral : 9.864 161.118 4966 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 4.01 % Allowed : 17.55 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 4166 helix: -0.12 (0.12), residues: 1828 sheet: -1.78 (0.25), residues: 394 loop : -1.48 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 34 TYR 0.026 0.002 TYR I 36 PHE 0.019 0.002 PHE G 238 TRP 0.024 0.001 TRP q 89 HIS 0.009 0.001 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (35072) covalent geometry : angle 0.75593 / 0.39 (47524) SS BOND : bond 0.01131 / 0.59 ( 4) SS BOND : angle 4.96309 / 2.89 ( 8) hydrogen bonds : bond 0.04829 / 3.11 ( 1334) hydrogen bonds : angle 5.44651 / 3.89 ( 3777) metal coordination : bond 0.02982 / 1.95 ( 37) metal coordination : angle 15.31521 / 11.63 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 854 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8069 (mm) REVERT: B 83 ASN cc_start: 0.8438 (m-40) cc_final: 0.8154 (m-40) REVERT: B 170 TYR cc_start: 0.8160 (t80) cc_final: 0.7904 (t80) REVERT: C 150 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8791 (p) REVERT: C 168 GLU cc_start: 0.8421 (tt0) cc_final: 0.7895 (tt0) REVERT: C 210 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8070 (ttp80) REVERT: C 211 TYR cc_start: 0.9254 (t80) cc_final: 0.8900 (t80) REVERT: D 95 LEU cc_start: 0.8885 (tp) cc_final: 0.8457 (tp) REVERT: D 97 LEU cc_start: 0.8876 (tp) cc_final: 0.8579 (tt) REVERT: D 110 ASP cc_start: 0.8397 (p0) cc_final: 0.8191 (p0) REVERT: D 389 TYR cc_start: 0.8329 (m-10) cc_final: 0.7998 (m-80) REVERT: D 443 MET cc_start: 0.8998 (mtm) cc_final: 0.8698 (mtm) REVERT: D 463 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7357 (ptt90) REVERT: E 147 ILE cc_start: 0.9121 (mm) cc_final: 0.8915 (mm) REVERT: E 151 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8677 (mm) REVERT: E 165 ASP cc_start: 0.8533 (t70) cc_final: 0.8131 (p0) REVERT: E 189 ASP cc_start: 0.8507 (m-30) cc_final: 0.7148 (t0) REVERT: F 71 LYS cc_start: 0.8752 (mmpt) cc_final: 0.8241 (mttt) REVERT: F 75 TRP cc_start: 0.8383 (t60) cc_final: 0.8093 (t60) REVERT: F 170 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: F 208 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7670 (tm-30) REVERT: F 233 VAL cc_start: 0.9243 (t) cc_final: 0.9026 (p) REVERT: F 291 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6647 (pt0) REVERT: G 37 ASP cc_start: 0.8316 (t0) cc_final: 0.7839 (t0) REVERT: G 172 ILE cc_start: 0.9129 (mt) cc_final: 0.8793 (mm) REVERT: G 197 THR cc_start: 0.8877 (p) cc_final: 0.8615 (p) REVERT: G 304 GLU cc_start: 0.8394 (tt0) cc_final: 0.8049 (tt0) REVERT: G 316 TYR cc_start: 0.8356 (m-80) cc_final: 0.7094 (m-80) REVERT: G 349 GLU cc_start: 0.8545 (mp0) cc_final: 0.8324 (mp0) REVERT: G 496 MET cc_start: 0.8612 (tpp) cc_final: 0.8350 (tpp) REVERT: G 579 MET cc_start: 0.8152 (ptp) cc_final: 0.7947 (ptm) REVERT: G 652 ASN cc_start: 0.8705 (p0) cc_final: 0.8456 (p0) REVERT: H 17 MET cc_start: 0.8657 (tmm) cc_final: 0.8433 (tmm) REVERT: H 59 GLU cc_start: 0.8544 (tt0) cc_final: 0.8305 (tt0) REVERT: H 61 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7232 (ttt) REVERT: H 87 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8920 (t) REVERT: H 183 MET cc_start: 0.8796 (mmt) cc_final: 0.8389 (mmt) REVERT: H 253 GLU cc_start: 0.8097 (pm20) cc_final: 0.7824 (pp20) REVERT: H 302 MET cc_start: 0.8626 (mtt) cc_final: 0.8313 (mtt) REVERT: H 318 MET cc_start: 0.7091 (mtm) cc_final: 0.6785 (tmm) REVERT: I 56 ASN cc_start: 0.8851 (t0) cc_final: 0.8224 (t0) REVERT: I 89 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: P 84 TYR cc_start: 0.9291 (p90) cc_final: 0.9053 (p90) REVERT: P 177 SER cc_start: 0.8986 (t) cc_final: 0.8783 (p) REVERT: P 210 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: P 362 LEU cc_start: 0.7580 (mt) cc_final: 0.7086 (mt) REVERT: Q 91 VAL cc_start: 0.8954 (p) cc_final: 0.8740 (t) REVERT: S 19 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9035 (pt) REVERT: S 57 GLU cc_start: 0.7565 (tp30) cc_final: 0.7322 (tp30) REVERT: S 79 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7244 (pp) REVERT: T 80 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8544 (tptt) REVERT: T 90 TYR cc_start: 0.7833 (t80) cc_final: 0.6479 (t80) REVERT: T 104 PHE cc_start: 0.7792 (m-80) cc_final: 0.7101 (m-80) REVERT: T 111 ASP cc_start: 0.8424 (t0) cc_final: 0.8010 (t0) REVERT: T 114 ASP cc_start: 0.8515 (m-30) cc_final: 0.7612 (m-30) REVERT: T 143 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8215 (mp0) REVERT: V 67 LYS cc_start: 0.9101 (tptt) cc_final: 0.8597 (ttmt) REVERT: V 94 MET cc_start: 0.9079 (tpp) cc_final: 0.8812 (tpp) REVERT: W 27 ASP cc_start: 0.8095 (m-30) cc_final: 0.7808 (p0) REVERT: W 43 TYR cc_start: 0.8698 (t80) cc_final: 0.7853 (t80) REVERT: W 54 GLN cc_start: 0.8667 (mt0) cc_final: 0.8198 (mm-40) REVERT: W 71 MET cc_start: 0.9082 (tpp) cc_final: 0.8745 (tpp) REVERT: W 102 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6875 (mm-40) REVERT: X 32 TYR cc_start: 0.9244 (t80) cc_final: 0.8962 (t80) REVERT: X 44 MET cc_start: 0.9059 (mmt) cc_final: 0.8552 (mmt) REVERT: X 77 HIS cc_start: 0.6338 (m-70) cc_final: 0.5777 (m90) REVERT: X 91 TYR cc_start: 0.8037 (t80) cc_final: 0.7294 (t80) REVERT: Z 80 ASP cc_start: 0.8336 (m-30) cc_final: 0.8135 (m-30) REVERT: Z 82 ARG cc_start: 0.5704 (mtt-85) cc_final: 0.5448 (mtt-85) REVERT: Z 103 ASN cc_start: 0.8054 (m-40) cc_final: 0.7831 (t0) REVERT: a 31 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8095 (m110) REVERT: a 35 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7591 (mt-10) REVERT: q 81 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.5274 (mpp) REVERT: q 93 MET cc_start: 0.8046 (mtt) cc_final: 0.7475 (mtt) REVERT: q 124 TYR cc_start: 0.7673 (t80) cc_final: 0.7402 (t80) REVERT: q 133 LYS cc_start: 0.7859 (ptmt) cc_final: 0.7347 (ptmt) outliers start: 147 outliers final: 76 residues processed: 943 average time/residue: 0.1888 time to fit residues: 294.8233 Evaluate side-chains 874 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 784 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 309 ASN Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain S residue 19 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain W residue 24 PHE Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 36 CYS Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain q residue 31 ASN Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 107 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 157 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 chunk 237 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 386 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN B 151 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN D 112 HIS F 116 ASN F 168 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 215 ASN P 219 ASN Q 88 GLN S 80 ASN V 110 ASN W 51 HIS W 94 GLN a 31 ASN a 58 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.136800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106369 restraints weight = 63562.951| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.75 r_work: 0.3311 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 35113 Z= 0.150 Angle : 0.941 64.425 47616 Z= 0.353 Chirality : 0.045 0.341 5191 Planarity : 0.005 0.077 6032 Dihedral : 9.477 160.614 4966 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 3.14 % Allowed : 18.83 % Favored : 78.03 % 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: -1.09 (0.13), residues: 4166 helix: 0.13 (0.12), residues: 1838 sheet: -1.62 (0.26), residues: 371 loop : -1.33 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 96 TYR 0.024 0.002 TYR a 60 PHE 0.025 0.002 PHE T 126 TRP 0.020 0.001 TRP q 89 HIS 0.007 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (35072) covalent geometry : angle 0.69238 / 0.35 (47524) SS BOND : bond 0.01591 / 0.83 ( 4) SS BOND : angle 1.84326 / 0.91 ( 8) hydrogen bonds : bond 0.04106 / 2.62 ( 1334) hydrogen bonds : angle 5.13391 / 3.65 ( 3777) metal coordination : bond 0.01891 / 1.32 ( 37) metal coordination : angle 15.17866 / 11.65 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 866 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9031 (tp) REVERT: A 105 GLU cc_start: 0.9452 (tt0) cc_final: 0.9240 (tt0) REVERT: B 83 ASN cc_start: 0.8441 (m-40) cc_final: 0.8232 (m-40) REVERT: B 170 TYR cc_start: 0.8043 (t80) cc_final: 0.7787 (t80) REVERT: C 150 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8692 (p) REVERT: C 168 GLU cc_start: 0.8388 (tt0) cc_final: 0.7887 (tt0) REVERT: C 211 TYR cc_start: 0.9217 (t80) cc_final: 0.8819 (t80) REVERT: D 95 LEU cc_start: 0.9000 (tp) cc_final: 0.8584 (tp) REVERT: D 208 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7759 (tm-30) REVERT: D 389 TYR cc_start: 0.8444 (m-10) cc_final: 0.8004 (m-10) REVERT: D 443 MET cc_start: 0.8994 (mtm) cc_final: 0.8709 (mtm) REVERT: D 463 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7417 (ptt90) REVERT: E 74 GLN cc_start: 0.8276 (pm20) cc_final: 0.7896 (pm20) REVERT: E 120 MET cc_start: 0.8865 (mmm) cc_final: 0.8561 (ttt) REVERT: E 147 ILE cc_start: 0.9088 (mm) cc_final: 0.8875 (mm) REVERT: E 151 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8636 (mm) REVERT: E 165 ASP cc_start: 0.8559 (t70) cc_final: 0.8205 (p0) REVERT: E 189 ASP cc_start: 0.8420 (m-30) cc_final: 0.7004 (t0) REVERT: E 192 TYR cc_start: 0.7873 (m-80) cc_final: 0.6872 (m-80) REVERT: F 51 TRP cc_start: 0.7008 (p-90) cc_final: 0.6730 (p-90) REVERT: F 71 LYS cc_start: 0.8756 (mmpt) cc_final: 0.8241 (mttt) REVERT: F 75 TRP cc_start: 0.8387 (t60) cc_final: 0.8152 (t60) REVERT: F 157 TYR cc_start: 0.6347 (t80) cc_final: 0.6145 (t80) REVERT: F 233 VAL cc_start: 0.9212 (t) cc_final: 0.9006 (p) REVERT: F 269 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7741 (mmm160) REVERT: G 37 ASP cc_start: 0.8298 (t0) cc_final: 0.7703 (t0) REVERT: G 145 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8276 (mtt) REVERT: G 172 ILE cc_start: 0.9092 (mt) cc_final: 0.8749 (mm) REVERT: G 197 THR cc_start: 0.8887 (p) cc_final: 0.8594 (p) REVERT: G 304 GLU cc_start: 0.8369 (tt0) cc_final: 0.8096 (tt0) REVERT: G 316 TYR cc_start: 0.8324 (m-80) cc_final: 0.7122 (m-80) REVERT: G 324 SER cc_start: 0.9043 (m) cc_final: 0.8582 (p) REVERT: G 380 ASP cc_start: 0.8160 (m-30) cc_final: 0.7713 (m-30) REVERT: G 496 MET cc_start: 0.8656 (tpp) cc_final: 0.8405 (tpp) REVERT: G 528 LEU cc_start: 0.9481 (mt) cc_final: 0.9244 (mt) REVERT: G 530 TYR cc_start: 0.8698 (m-80) cc_final: 0.8183 (m-80) REVERT: H 59 GLU cc_start: 0.8480 (tt0) cc_final: 0.7879 (tt0) REVERT: H 87 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8901 (t) REVERT: H 163 GLN cc_start: 0.8360 (tp40) cc_final: 0.7802 (tm-30) REVERT: H 192 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: H 249 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7817 (tp) REVERT: H 302 MET cc_start: 0.8773 (mtt) cc_final: 0.8461 (mtt) REVERT: H 318 MET cc_start: 0.7181 (mtm) cc_final: 0.6913 (tmm) REVERT: I 56 ASN cc_start: 0.8838 (t0) cc_final: 0.8476 (t0) REVERT: I 70 LEU cc_start: 0.8951 (mt) cc_final: 0.8688 (mt) REVERT: I 89 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: P 84 TYR cc_start: 0.9263 (p90) cc_final: 0.9044 (p90) REVERT: P 177 SER cc_start: 0.9024 (t) cc_final: 0.8817 (p) REVERT: P 210 GLU cc_start: 0.8122 (pm20) cc_final: 0.7837 (pm20) REVERT: P 261 LYS cc_start: 0.7671 (mttt) cc_final: 0.7129 (tptp) REVERT: Q 135 ILE cc_start: 0.9354 (mm) cc_final: 0.9139 (mt) REVERT: R 90 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8865 (ttpt) REVERT: S 50 ASN cc_start: 0.8595 (m-40) cc_final: 0.7427 (t0) REVERT: S 57 GLU cc_start: 0.7223 (tp30) cc_final: 0.6968 (tp30) REVERT: S 79 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7451 (pp) REVERT: S 80 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8189 (t0) REVERT: T 80 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8434 (tptt) REVERT: T 81 ASP cc_start: 0.8923 (t0) cc_final: 0.8590 (m-30) REVERT: T 84 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8719 (mt) REVERT: T 90 TYR cc_start: 0.7458 (t80) cc_final: 0.6586 (t80) REVERT: T 104 PHE cc_start: 0.7888 (m-10) cc_final: 0.7092 (m-80) REVERT: T 107 ASP cc_start: 0.7094 (m-30) cc_final: 0.6733 (m-30) REVERT: T 111 ASP cc_start: 0.8473 (t0) cc_final: 0.8076 (t0) REVERT: T 113 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7777 (mt) REVERT: T 114 ASP cc_start: 0.8493 (m-30) cc_final: 0.7945 (m-30) REVERT: T 143 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8478 (mp0) REVERT: V 57 ASP cc_start: 0.8699 (m-30) cc_final: 0.8441 (m-30) REVERT: V 67 LYS cc_start: 0.9104 (tptt) cc_final: 0.8610 (ttmm) REVERT: W 27 ASP cc_start: 0.8015 (m-30) cc_final: 0.7632 (p0) REVERT: W 43 TYR cc_start: 0.8713 (t80) cc_final: 0.7926 (t80) REVERT: W 54 GLN cc_start: 0.8635 (mt0) cc_final: 0.8128 (mm-40) REVERT: W 97 ILE cc_start: 0.9209 (tt) cc_final: 0.8960 (pt) REVERT: W 102 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6906 (mm-40) REVERT: X 44 MET cc_start: 0.9033 (mmt) cc_final: 0.8808 (mmt) REVERT: X 77 HIS cc_start: 0.6727 (m-70) cc_final: 0.6526 (m170) REVERT: X 91 TYR cc_start: 0.8040 (t80) cc_final: 0.7658 (t80) REVERT: Z 80 ASP cc_start: 0.8384 (m-30) cc_final: 0.8074 (m-30) REVERT: Z 103 ASN cc_start: 0.8014 (m-40) cc_final: 0.7572 (p0) REVERT: a 35 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7603 (mt-10) REVERT: a 66 LEU cc_start: 0.8748 (mm) cc_final: 0.8432 (mp) REVERT: q 81 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.5291 (mpp) REVERT: q 93 MET cc_start: 0.7869 (mtt) cc_final: 0.7350 (mtt) REVERT: q 124 TYR cc_start: 0.7632 (t80) cc_final: 0.7431 (t80) outliers start: 115 outliers final: 61 residues processed: 936 average time/residue: 0.1909 time to fit residues: 293.7964 Evaluate side-chains 860 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 785 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 309 ASN Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 113 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 110 ASN Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 52 optimal weight: 0.6980 chunk 250 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 297 optimal weight: 0.0060 chunk 239 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 367 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN B 166 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN D 442 HIS ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 705 GLN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN V 110 ASN W 51 HIS X 31 HIS ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 110 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.137206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.108600 restraints weight = 63740.218| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.60 r_work: 0.3341 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 35113 Z= 0.139 Angle : 0.952 65.401 47616 Z= 0.347 Chirality : 0.044 0.319 5191 Planarity : 0.005 0.080 6032 Dihedral : 9.120 158.066 4966 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer: Outliers : 3.14 % Allowed : 19.98 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 4166 helix: 0.28 (0.12), residues: 1838 sheet: -1.59 (0.26), residues: 371 loop : -1.26 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 40 TYR 0.025 0.002 TYR T 147 PHE 0.025 0.001 PHE F 276 TRP 0.018 0.001 TRP q 89 HIS 0.011 0.001 HIS P 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (35072) covalent geometry : angle 0.68221 / 0.34 (47524) SS BOND : bond 0.00594 / 0.31 ( 4) SS BOND : angle 4.64717 / 2.65 ( 8) hydrogen bonds : bond 0.03937 / 2.53 ( 1334) hydrogen bonds : angle 5.01411 / 3.58 ( 3777) metal coordination : bond 0.01695 / 1.20 ( 37) metal coordination : angle 15.76535 / 12.25 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 823 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8919 (tt) REVERT: B 83 ASN cc_start: 0.8430 (m-40) cc_final: 0.8132 (m-40) REVERT: B 104 MET cc_start: 0.7928 (tpt) cc_final: 0.7722 (tpt) REVERT: B 170 TYR cc_start: 0.7966 (t80) cc_final: 0.7695 (t80) REVERT: C 168 GLU cc_start: 0.8281 (tt0) cc_final: 0.7810 (tt0) REVERT: C 211 TYR cc_start: 0.9192 (t80) cc_final: 0.8806 (t80) REVERT: D 95 LEU cc_start: 0.9005 (tp) cc_final: 0.8578 (tp) REVERT: D 208 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 389 TYR cc_start: 0.8433 (m-10) cc_final: 0.8016 (m-10) REVERT: D 443 MET cc_start: 0.8990 (mtm) cc_final: 0.8715 (mtm) REVERT: D 463 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7376 (ptt90) REVERT: E 120 MET cc_start: 0.8879 (mmm) cc_final: 0.8583 (ttt) REVERT: E 147 ILE cc_start: 0.9089 (mm) cc_final: 0.8870 (mm) REVERT: E 151 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8627 (mm) REVERT: E 186 GLN cc_start: 0.8714 (tp-100) cc_final: 0.8290 (tp40) REVERT: E 192 TYR cc_start: 0.7754 (m-80) cc_final: 0.6887 (m-80) REVERT: F 53 LEU cc_start: 0.8641 (tt) cc_final: 0.8368 (tt) REVERT: F 71 LYS cc_start: 0.8709 (mmpt) cc_final: 0.8248 (mttt) REVERT: F 75 TRP cc_start: 0.8409 (t60) cc_final: 0.8132 (t60) REVERT: F 269 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7311 (mmm160) REVERT: G 37 ASP cc_start: 0.8252 (t0) cc_final: 0.7599 (t0) REVERT: G 145 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8041 (mtp) REVERT: G 172 ILE cc_start: 0.9050 (mt) cc_final: 0.8697 (mm) REVERT: G 197 THR cc_start: 0.8861 (p) cc_final: 0.8558 (p) REVERT: G 304 GLU cc_start: 0.8249 (tt0) cc_final: 0.7914 (tt0) REVERT: G 316 TYR cc_start: 0.8279 (m-80) cc_final: 0.7019 (m-80) REVERT: G 324 SER cc_start: 0.9031 (m) cc_final: 0.8579 (p) REVERT: G 380 ASP cc_start: 0.7737 (m-30) cc_final: 0.7413 (m-30) REVERT: G 410 GLU cc_start: 0.8376 (tt0) cc_final: 0.8038 (tt0) REVERT: G 496 MET cc_start: 0.8781 (tpp) cc_final: 0.8504 (tpp) REVERT: G 530 TYR cc_start: 0.8590 (m-80) cc_final: 0.8201 (m-80) REVERT: G 660 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7747 (mm-30) REVERT: G 696 MET cc_start: 0.8655 (mtm) cc_final: 0.8409 (mtt) REVERT: H 59 GLU cc_start: 0.8412 (tt0) cc_final: 0.7860 (tt0) REVERT: H 87 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8899 (t) REVERT: H 130 PHE cc_start: 0.8197 (t80) cc_final: 0.7960 (t80) REVERT: H 163 GLN cc_start: 0.8297 (tp40) cc_final: 0.7832 (tm-30) REVERT: H 253 GLU cc_start: 0.8058 (pm20) cc_final: 0.7802 (pp20) REVERT: H 302 MET cc_start: 0.8763 (mtt) cc_final: 0.8482 (mtt) REVERT: H 318 MET cc_start: 0.7216 (mtm) cc_final: 0.6774 (tmm) REVERT: I 56 ASN cc_start: 0.8861 (t0) cc_final: 0.8489 (t0) REVERT: I 191 LEU cc_start: 0.8740 (mt) cc_final: 0.8510 (mt) REVERT: P 84 TYR cc_start: 0.9232 (p90) cc_final: 0.8995 (p90) REVERT: P 128 ASN cc_start: 0.8225 (t0) cc_final: 0.7923 (t0) REVERT: P 134 TRP cc_start: 0.8277 (p90) cc_final: 0.8074 (p90) REVERT: P 177 SER cc_start: 0.8979 (t) cc_final: 0.8774 (p) REVERT: P 210 GLU cc_start: 0.8128 (pm20) cc_final: 0.7843 (pm20) REVERT: P 261 LYS cc_start: 0.7683 (mttt) cc_final: 0.7167 (tptp) REVERT: Q 108 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7925 (tp30) REVERT: Q 135 ILE cc_start: 0.9343 (mm) cc_final: 0.9142 (mt) REVERT: R 90 LYS cc_start: 0.9106 (ttmm) cc_final: 0.8895 (ttpt) REVERT: S 23 LEU cc_start: 0.8183 (pp) cc_final: 0.7891 (pp) REVERT: S 79 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7245 (pp) REVERT: S 80 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8092 (t0) REVERT: T 81 ASP cc_start: 0.8949 (t0) cc_final: 0.8560 (m-30) REVERT: T 82 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7753 (mtm110) REVERT: T 90 TYR cc_start: 0.7571 (t80) cc_final: 0.6756 (t80) REVERT: T 104 PHE cc_start: 0.7752 (m-10) cc_final: 0.7140 (m-80) REVERT: T 111 ASP cc_start: 0.8289 (t0) cc_final: 0.7994 (t0) REVERT: T 113 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7377 (mt) REVERT: T 114 ASP cc_start: 0.8556 (m-30) cc_final: 0.7853 (m-30) REVERT: T 143 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8378 (mp0) REVERT: V 57 ASP cc_start: 0.8738 (m-30) cc_final: 0.8434 (m-30) REVERT: V 67 LYS cc_start: 0.9052 (tptt) cc_final: 0.8579 (ttmm) REVERT: W 26 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.7415 (mtp85) REVERT: W 27 ASP cc_start: 0.7956 (m-30) cc_final: 0.7653 (p0) REVERT: W 37 GLU cc_start: 0.9209 (tt0) cc_final: 0.9002 (tt0) REVERT: W 43 TYR cc_start: 0.8670 (t80) cc_final: 0.7805 (t80) REVERT: W 54 GLN cc_start: 0.8634 (mt0) cc_final: 0.8108 (mm-40) REVERT: W 97 ILE cc_start: 0.9172 (tt) cc_final: 0.8972 (pt) REVERT: W 102 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6945 (mm-40) REVERT: X 77 HIS cc_start: 0.6938 (m-70) cc_final: 0.6517 (m170) REVERT: X 91 TYR cc_start: 0.8088 (t80) cc_final: 0.7454 (t80) REVERT: Z 80 ASP cc_start: 0.8287 (m-30) cc_final: 0.7980 (m-30) REVERT: Z 103 ASN cc_start: 0.7984 (m-40) cc_final: 0.7577 (p0) REVERT: a 35 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7432 (mt-10) REVERT: a 66 LEU cc_start: 0.8728 (mm) cc_final: 0.8519 (mt) REVERT: q 33 ILE cc_start: 0.4831 (OUTLIER) cc_final: 0.4549 (mm) REVERT: q 81 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5080 (mpp) REVERT: q 93 MET cc_start: 0.7972 (mtt) cc_final: 0.7466 (mtt) REVERT: q 132 LYS cc_start: 0.7995 (tttt) cc_final: 0.7778 (tttm) outliers start: 115 outliers final: 68 residues processed: 893 average time/residue: 0.1824 time to fit residues: 268.4554 Evaluate side-chains 833 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 755 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 309 ASN Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 113 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain r residue 31 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 305 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 297 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 404 optimal weight: 8.9990 chunk 360 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 GLN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 GLN S 80 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 HIS Z 55 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN b 71 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099328 restraints weight = 64728.454| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.03 r_work: 0.3178 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 35113 Z= 0.278 Angle : 1.060 75.234 47616 Z= 0.390 Chirality : 0.049 0.363 5191 Planarity : 0.006 0.081 6032 Dihedral : 9.185 162.850 4966 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 3.90 % Allowed : 19.54 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 4166 helix: 0.24 (0.12), residues: 1846 sheet: -1.62 (0.25), residues: 400 loop : -1.31 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 52 TYR 0.030 0.002 TYR I 76 PHE 0.024 0.002 PHE P 213 TRP 0.020 0.002 TRP A 77 HIS 0.012 0.002 HIS R 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.28 (35072) covalent geometry : angle 0.75957 / 0.38 (47524) SS BOND : bond 0.00837 / 0.44 ( 4) SS BOND : angle 3.80051 / 2.16 ( 8) hydrogen bonds : bond 0.04356 / 2.80 ( 1334) hydrogen bonds : angle 5.12331 / 3.66 ( 3777) metal coordination : bond 0.03442 / 2.26 ( 37) metal coordination : angle 17.56964 / 13.29 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 754 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9054 (mp) REVERT: B 83 ASN cc_start: 0.8623 (m-40) cc_final: 0.8299 (m-40) REVERT: B 104 MET cc_start: 0.8127 (tpt) cc_final: 0.7898 (tpt) REVERT: B 161 MET cc_start: 0.9051 (tpp) cc_final: 0.8532 (ttt) REVERT: B 211 LYS cc_start: 0.8847 (tttp) cc_final: 0.8588 (tttt) REVERT: C 168 GLU cc_start: 0.8554 (tt0) cc_final: 0.8127 (tt0) REVERT: D 97 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8643 (tt) REVERT: D 371 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8662 (ttp) REVERT: D 443 MET cc_start: 0.9061 (mtm) cc_final: 0.8805 (mtm) REVERT: D 463 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7674 (ptt90) REVERT: E 120 MET cc_start: 0.8982 (mmm) cc_final: 0.8614 (ttt) REVERT: E 147 ILE cc_start: 0.9040 (mm) cc_final: 0.8829 (mm) REVERT: E 151 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8666 (mm) REVERT: F 53 LEU cc_start: 0.8786 (tt) cc_final: 0.8515 (tp) REVERT: F 75 TRP cc_start: 0.8592 (t60) cc_final: 0.8245 (t60) REVERT: F 170 GLN cc_start: 0.8424 (mt0) cc_final: 0.8046 (tm-30) REVERT: F 269 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7578 (tpm170) REVERT: G 37 ASP cc_start: 0.8525 (t0) cc_final: 0.8268 (t0) REVERT: G 145 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8242 (mtt) REVERT: G 172 ILE cc_start: 0.9235 (mt) cc_final: 0.8886 (mm) REVERT: G 197 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8581 (p) REVERT: G 304 GLU cc_start: 0.8461 (tt0) cc_final: 0.8218 (tt0) REVERT: G 316 TYR cc_start: 0.8409 (m-80) cc_final: 0.7130 (m-80) REVERT: G 324 SER cc_start: 0.9153 (m) cc_final: 0.8706 (p) REVERT: G 380 ASP cc_start: 0.7934 (m-30) cc_final: 0.7702 (m-30) REVERT: G 496 MET cc_start: 0.8900 (tpp) cc_final: 0.8616 (tpp) REVERT: G 579 MET cc_start: 0.8083 (ptp) cc_final: 0.7859 (ptm) REVERT: G 658 ASP cc_start: 0.8143 (t0) cc_final: 0.7915 (t0) REVERT: G 660 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7627 (mm-30) REVERT: H 31 MET cc_start: 0.9100 (mtt) cc_final: 0.8899 (mtt) REVERT: H 130 PHE cc_start: 0.8497 (t80) cc_final: 0.8197 (t80) REVERT: H 163 GLN cc_start: 0.8372 (tp40) cc_final: 0.7820 (tm-30) REVERT: H 184 MET cc_start: 0.8747 (mtp) cc_final: 0.8351 (mtp) REVERT: H 253 GLU cc_start: 0.8380 (pm20) cc_final: 0.8089 (pp20) REVERT: H 277 TYR cc_start: 0.9120 (m-80) cc_final: 0.8556 (m-80) REVERT: H 282 TYR cc_start: 0.8930 (t80) cc_final: 0.8672 (t80) REVERT: H 302 MET cc_start: 0.8989 (mtt) cc_final: 0.8755 (mtt) REVERT: I 137 ASP cc_start: 0.8387 (t0) cc_final: 0.8050 (m-30) REVERT: P 210 GLU cc_start: 0.8354 (pm20) cc_final: 0.8000 (pm20) REVERT: P 362 LEU cc_start: 0.7636 (mt) cc_final: 0.7185 (mt) REVERT: Q 73 LYS cc_start: 0.9193 (mtmt) cc_final: 0.8862 (mtmm) REVERT: Q 91 VAL cc_start: 0.8990 (p) cc_final: 0.8786 (t) REVERT: Q 166 TRP cc_start: 0.5042 (m-10) cc_final: 0.4741 (m-10) REVERT: R 75 ARG cc_start: 0.7374 (mmp80) cc_final: 0.7055 (tpp-160) REVERT: S 17 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7383 (mmt-90) REVERT: S 51 LEU cc_start: 0.9238 (tt) cc_final: 0.9028 (tt) REVERT: S 79 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7292 (pp) REVERT: T 80 LYS cc_start: 0.8193 (tppt) cc_final: 0.7876 (tttp) REVERT: T 81 ASP cc_start: 0.9002 (t0) cc_final: 0.8617 (m-30) REVERT: T 84 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8699 (mt) REVERT: T 90 TYR cc_start: 0.7664 (t80) cc_final: 0.6572 (t80) REVERT: T 104 PHE cc_start: 0.7853 (m-10) cc_final: 0.7148 (m-80) REVERT: T 111 ASP cc_start: 0.8411 (t0) cc_final: 0.8015 (t0) REVERT: T 114 ASP cc_start: 0.8638 (m-30) cc_final: 0.8199 (m-30) REVERT: T 143 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8329 (mp0) REVERT: V 57 ASP cc_start: 0.8839 (m-30) cc_final: 0.8500 (m-30) REVERT: W 43 TYR cc_start: 0.8775 (t80) cc_final: 0.7958 (t80) REVERT: W 54 GLN cc_start: 0.8664 (mt0) cc_final: 0.8127 (mm-40) REVERT: W 68 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8338 (tm-30) REVERT: W 99 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7201 (t) REVERT: W 102 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6685 (mm-40) REVERT: X 55 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7873 (mtt-85) REVERT: Z 27 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7544 (mpt180) REVERT: Z 103 ASN cc_start: 0.8074 (m-40) cc_final: 0.7670 (p0) REVERT: a 35 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7817 (mt-10) REVERT: q 33 ILE cc_start: 0.4820 (OUTLIER) cc_final: 0.4532 (mm) REVERT: q 81 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5118 (mpp) REVERT: q 124 TYR cc_start: 0.7621 (t80) cc_final: 0.7411 (t80) REVERT: r 11 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7137 (tt) outliers start: 143 outliers final: 96 residues processed: 843 average time/residue: 0.2056 time to fit residues: 286.1456 Evaluate side-chains 827 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 717 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 309 ASN Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 107 SER Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 97 optimal weight: 7.9990 chunk 323 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 231 optimal weight: 0.5980 chunk 220 optimal weight: 0.0470 chunk 41 optimal weight: 0.0470 chunk 318 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN F 116 ASN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 569 GLN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN P 72 HIS ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 HIS W 94 GLN a 58 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.134442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103268 restraints weight = 64754.558| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.92 r_work: 0.3281 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35113 Z= 0.133 Angle : 0.958 68.573 47616 Z= 0.340 Chirality : 0.044 0.310 5191 Planarity : 0.005 0.083 6032 Dihedral : 9.032 163.845 4966 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.09 % Rotamer: Outliers : 2.81 % Allowed : 21.42 % Favored : 75.76 % 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: -0.75 (0.13), residues: 4166 helix: 0.46 (0.12), residues: 1846 sheet: -1.43 (0.27), residues: 374 loop : -1.20 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG W 117 TYR 0.040 0.002 TYR P 84 PHE 0.026 0.001 PHE G 409 TRP 0.030 0.001 TRP q 89 HIS 0.009 0.001 HIS P 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (35072) covalent geometry : angle 0.66845 / 0.33 (47524) SS BOND : bond 0.00428 / 0.22 ( 4) SS BOND : angle 1.57276 / 0.77 ( 8) hydrogen bonds : bond 0.03764 / 2.42 ( 1334) hydrogen bonds : angle 4.90989 / 3.50 ( 3777) metal coordination : bond 0.01627 / 1.16 ( 37) metal coordination : angle 16.34464 / 12.68 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 800 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TRP cc_start: 0.7249 (t60) cc_final: 0.6530 (t60) REVERT: B 83 ASN cc_start: 0.8436 (m-40) cc_final: 0.8149 (m-40) REVERT: B 104 MET cc_start: 0.7929 (tpt) cc_final: 0.7693 (tpt) REVERT: B 170 TYR cc_start: 0.7969 (t80) cc_final: 0.7716 (t80) REVERT: C 168 GLU cc_start: 0.8411 (tt0) cc_final: 0.7906 (tt0) REVERT: C 211 TYR cc_start: 0.9271 (t80) cc_final: 0.8809 (t80) REVERT: D 95 LEU cc_start: 0.9071 (tp) cc_final: 0.8594 (tp) REVERT: D 389 TYR cc_start: 0.8647 (m-10) cc_final: 0.7723 (m-10) REVERT: D 443 MET cc_start: 0.9013 (mtm) cc_final: 0.8793 (mtm) REVERT: D 463 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7649 (ptt90) REVERT: E 61 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7261 (mtm-85) REVERT: E 120 MET cc_start: 0.8917 (mmm) cc_final: 0.8542 (ttp) REVERT: E 147 ILE cc_start: 0.9041 (mm) cc_final: 0.8833 (mm) REVERT: E 151 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8580 (mm) REVERT: E 192 TYR cc_start: 0.7556 (m-80) cc_final: 0.6571 (m-80) REVERT: F 53 LEU cc_start: 0.8747 (tt) cc_final: 0.8491 (tp) REVERT: F 75 TRP cc_start: 0.8566 (t60) cc_final: 0.8342 (t60) REVERT: F 102 MET cc_start: 0.7243 (ptm) cc_final: 0.6983 (ttp) REVERT: F 157 TYR cc_start: 0.5994 (t80) cc_final: 0.5624 (t80) REVERT: F 226 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8381 (tppt) REVERT: F 269 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7551 (tpm170) REVERT: G 37 ASP cc_start: 0.8554 (t0) cc_final: 0.8337 (t0) REVERT: G 145 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7927 (mtp) REVERT: G 172 ILE cc_start: 0.9068 (mt) cc_final: 0.8703 (mm) REVERT: G 197 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8532 (p) REVERT: G 304 GLU cc_start: 0.8316 (tt0) cc_final: 0.8052 (tt0) REVERT: G 316 TYR cc_start: 0.8343 (m-80) cc_final: 0.7062 (m-80) REVERT: G 324 SER cc_start: 0.9056 (m) cc_final: 0.8659 (p) REVERT: G 380 ASP cc_start: 0.7882 (m-30) cc_final: 0.7667 (m-30) REVERT: G 496 MET cc_start: 0.8993 (tpp) cc_final: 0.8706 (tpp) REVERT: G 530 TYR cc_start: 0.8696 (m-80) cc_final: 0.8132 (m-80) REVERT: G 660 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7930 (mm-30) REVERT: G 696 MET cc_start: 0.8669 (mtm) cc_final: 0.8416 (mtt) REVERT: H 59 GLU cc_start: 0.8557 (tt0) cc_final: 0.8286 (tt0) REVERT: H 130 PHE cc_start: 0.8420 (t80) cc_final: 0.8132 (t80) REVERT: H 184 MET cc_start: 0.8584 (mtp) cc_final: 0.8235 (mtp) REVERT: H 192 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7385 (tm-30) REVERT: H 202 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6486 (tm-30) REVERT: H 253 GLU cc_start: 0.8140 (pm20) cc_final: 0.7868 (pp20) REVERT: H 277 TYR cc_start: 0.9041 (m-80) cc_final: 0.8443 (m-80) REVERT: H 282 TYR cc_start: 0.8668 (t80) cc_final: 0.8442 (t80) REVERT: H 302 MET cc_start: 0.8821 (mtt) cc_final: 0.8581 (mtt) REVERT: P 107 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8652 (mp0) REVERT: P 128 ASN cc_start: 0.8303 (t0) cc_final: 0.8012 (t0) REVERT: P 175 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7613 (pttt) REVERT: P 210 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: P 362 LEU cc_start: 0.7672 (mt) cc_final: 0.7247 (mt) REVERT: Q 73 LYS cc_start: 0.9139 (mtmt) cc_final: 0.8816 (mtmm) REVERT: Q 91 VAL cc_start: 0.8848 (p) cc_final: 0.8641 (t) REVERT: Q 149 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8549 (mm-30) REVERT: Q 166 TRP cc_start: 0.4964 (m-10) cc_final: 0.4597 (m-10) REVERT: S 17 ARG cc_start: 0.7512 (mmm160) cc_final: 0.7133 (mmt-90) REVERT: S 79 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7247 (pp) REVERT: T 80 LYS cc_start: 0.8166 (tppt) cc_final: 0.7843 (tptm) REVERT: T 81 ASP cc_start: 0.8976 (t0) cc_final: 0.8579 (m-30) REVERT: T 84 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8682 (mt) REVERT: T 90 TYR cc_start: 0.7818 (t80) cc_final: 0.6647 (t80) REVERT: T 104 PHE cc_start: 0.7797 (m-10) cc_final: 0.7327 (m-80) REVERT: T 114 ASP cc_start: 0.8618 (m-30) cc_final: 0.8256 (m-30) REVERT: T 143 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8438 (mp0) REVERT: V 34 ILE cc_start: 0.8584 (tp) cc_final: 0.8360 (tp) REVERT: V 57 ASP cc_start: 0.8750 (m-30) cc_final: 0.8357 (m-30) REVERT: V 83 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8682 (tp40) REVERT: W 43 TYR cc_start: 0.8586 (t80) cc_final: 0.7939 (t80) REVERT: W 51 HIS cc_start: 0.8648 (t-170) cc_final: 0.8440 (t-90) REVERT: W 54 GLN cc_start: 0.8575 (mt0) cc_final: 0.8006 (mm-40) REVERT: W 68 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8268 (tm-30) REVERT: W 99 VAL cc_start: 0.7111 (OUTLIER) cc_final: 0.6874 (t) REVERT: W 102 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6814 (mm-40) REVERT: X 55 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7773 (mtt-85) REVERT: Z 103 ASN cc_start: 0.8132 (m-40) cc_final: 0.7702 (p0) REVERT: a 35 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7693 (mt-10) REVERT: b 51 TYR cc_start: 0.8407 (m-10) cc_final: 0.7805 (m-10) REVERT: q 33 ILE cc_start: 0.4635 (OUTLIER) cc_final: 0.4390 (mm) REVERT: q 81 MET cc_start: 0.6047 (OUTLIER) cc_final: 0.4988 (mpp) REVERT: q 124 TYR cc_start: 0.7418 (t80) cc_final: 0.7204 (t80) REVERT: r 11 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7140 (tt) outliers start: 103 outliers final: 73 residues processed: 862 average time/residue: 0.2041 time to fit residues: 290.3376 Evaluate side-chains 824 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 738 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 309 ASN Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 569 GLN Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain W residue 24 PHE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain r residue 8 ILE Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 124 optimal weight: 10.0000 chunk 169 optimal weight: 0.0170 chunk 78 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 378 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 369 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN ** r 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.133662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102161 restraints weight = 64686.814| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.73 r_work: 0.3262 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 35113 Z= 0.152 Angle : 0.969 69.800 47616 Z= 0.347 Chirality : 0.045 0.337 5191 Planarity : 0.005 0.081 6032 Dihedral : 8.906 163.274 4966 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer: Outliers : 3.19 % Allowed : 21.94 % Favored : 74.86 % 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: -0.72 (0.13), residues: 4166 helix: 0.51 (0.12), residues: 1848 sheet: -1.39 (0.27), residues: 368 loop : -1.22 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG W 117 TYR 0.031 0.002 TYR P 84 PHE 0.032 0.002 PHE G 409 TRP 0.045 0.001 TRP q 89 HIS 0.005 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (35072) covalent geometry : angle 0.68255 / 0.34 (47524) SS BOND : bond 0.00378 / 0.20 ( 4) SS BOND : angle 1.45651 / 0.72 ( 8) hydrogen bonds : bond 0.03737 / 2.39 ( 1334) hydrogen bonds : angle 4.85752 / 3.46 ( 3777) metal coordination : bond 0.01968 / 1.36 ( 37) metal coordination : angle 16.37367 / 12.69 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 753 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TRP cc_start: 0.7244 (t60) cc_final: 0.6488 (t60) REVERT: B 83 ASN cc_start: 0.8318 (m-40) cc_final: 0.8026 (m-40) REVERT: B 170 TYR cc_start: 0.7988 (t80) cc_final: 0.7751 (t80) REVERT: C 76 GLN cc_start: 0.8530 (pt0) cc_final: 0.8098 (pt0) REVERT: C 168 GLU cc_start: 0.8408 (tt0) cc_final: 0.7892 (tt0) REVERT: D 95 LEU cc_start: 0.9064 (tp) cc_final: 0.8593 (tp) REVERT: D 443 MET cc_start: 0.8973 (mtm) cc_final: 0.8704 (mtm) REVERT: D 463 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7655 (ptt90) REVERT: E 61 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7291 (mtm-85) REVERT: E 109 MET cc_start: 0.8814 (tpp) cc_final: 0.8410 (tpp) REVERT: E 120 MET cc_start: 0.8904 (mmm) cc_final: 0.8535 (ttt) REVERT: E 151 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8629 (mm) REVERT: E 167 LEU cc_start: 0.8319 (tp) cc_final: 0.7929 (tp) REVERT: E 192 TYR cc_start: 0.7343 (m-80) cc_final: 0.6200 (m-80) REVERT: F 53 LEU cc_start: 0.8750 (tt) cc_final: 0.8482 (tp) REVERT: F 75 TRP cc_start: 0.8662 (t60) cc_final: 0.8334 (t60) REVERT: F 157 TYR cc_start: 0.6251 (t80) cc_final: 0.5865 (t80) REVERT: F 226 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8372 (tppt) REVERT: F 269 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7529 (tpm170) REVERT: F 450 MET cc_start: 0.8197 (mmp) cc_final: 0.7762 (mmt) REVERT: G 37 ASP cc_start: 0.8514 (t0) cc_final: 0.8309 (t0) REVERT: G 145 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8498 (mmm) REVERT: G 172 ILE cc_start: 0.9073 (mt) cc_final: 0.8694 (mm) REVERT: G 197 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8582 (p) REVERT: G 295 ASP cc_start: 0.8321 (p0) cc_final: 0.8047 (p0) REVERT: G 304 GLU cc_start: 0.8331 (tt0) cc_final: 0.8016 (tt0) REVERT: G 316 TYR cc_start: 0.8337 (m-80) cc_final: 0.7085 (m-80) REVERT: G 324 SER cc_start: 0.9114 (m) cc_final: 0.8700 (p) REVERT: G 380 ASP cc_start: 0.7873 (m-30) cc_final: 0.7623 (m-30) REVERT: G 496 MET cc_start: 0.9015 (tpp) cc_final: 0.8778 (tpp) REVERT: G 530 TYR cc_start: 0.8688 (m-80) cc_final: 0.8153 (m-80) REVERT: G 660 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7948 (mm-30) REVERT: G 696 MET cc_start: 0.8635 (mtm) cc_final: 0.8396 (mtt) REVERT: H 59 GLU cc_start: 0.8485 (tt0) cc_final: 0.8167 (tt0) REVERT: H 130 PHE cc_start: 0.8407 (t80) cc_final: 0.8090 (t80) REVERT: H 184 MET cc_start: 0.8591 (mtp) cc_final: 0.8277 (mtp) REVERT: H 253 GLU cc_start: 0.8148 (pm20) cc_final: 0.7929 (pp20) REVERT: H 274 ARG cc_start: 0.9181 (ttt90) cc_final: 0.8930 (ttm-80) REVERT: H 277 TYR cc_start: 0.9052 (m-80) cc_final: 0.8453 (m-80) REVERT: H 282 TYR cc_start: 0.8633 (t80) cc_final: 0.8419 (t80) REVERT: H 302 MET cc_start: 0.8825 (mtt) cc_final: 0.8598 (mtt) REVERT: P 107 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8651 (mp0) REVERT: P 128 ASN cc_start: 0.8329 (t0) cc_final: 0.8015 (t0) REVERT: P 205 ASP cc_start: 0.8157 (m-30) cc_final: 0.7853 (t0) REVERT: P 210 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: P 214 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8337 (tp) REVERT: P 283 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7484 (mmm) REVERT: P 362 LEU cc_start: 0.7659 (mt) cc_final: 0.7157 (mt) REVERT: Q 71 HIS cc_start: 0.8707 (m90) cc_final: 0.8445 (m-70) REVERT: Q 73 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8822 (mtmm) REVERT: Q 166 TRP cc_start: 0.4954 (m-10) cc_final: 0.4745 (m-10) REVERT: S 17 ARG cc_start: 0.7558 (mmm160) cc_final: 0.7147 (mmt-90) REVERT: S 25 GLN cc_start: 0.8388 (tt0) cc_final: 0.8125 (tt0) REVERT: S 79 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7216 (pp) REVERT: S 89 ARG cc_start: 0.8347 (mtp180) cc_final: 0.8028 (mtm180) REVERT: T 81 ASP cc_start: 0.8950 (t0) cc_final: 0.8502 (m-30) REVERT: T 90 TYR cc_start: 0.7804 (t80) cc_final: 0.7396 (t80) REVERT: T 143 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8414 (mp0) REVERT: V 34 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8367 (tp) REVERT: V 57 ASP cc_start: 0.8777 (m-30) cc_final: 0.8367 (m-30) REVERT: V 83 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8682 (tp40) REVERT: W 51 HIS cc_start: 0.8673 (t-170) cc_final: 0.8473 (t-90) REVERT: W 54 GLN cc_start: 0.8625 (mt0) cc_final: 0.8074 (mm-40) REVERT: W 68 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8287 (tm-30) REVERT: W 99 VAL cc_start: 0.7056 (OUTLIER) cc_final: 0.6824 (t) REVERT: W 102 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6728 (mm-40) REVERT: X 55 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7740 (mtt-85) REVERT: Z 80 ASP cc_start: 0.8199 (m-30) cc_final: 0.7977 (m-30) REVERT: Z 103 ASN cc_start: 0.8056 (m-40) cc_final: 0.7692 (p0) REVERT: a 35 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7707 (mt-10) REVERT: a 55 SER cc_start: 0.7377 (m) cc_final: 0.7113 (p) REVERT: b 51 TYR cc_start: 0.8438 (m-10) cc_final: 0.7773 (m-10) REVERT: q 33 ILE cc_start: 0.4618 (OUTLIER) cc_final: 0.4362 (mm) REVERT: q 81 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5087 (mpp) REVERT: q 133 LYS cc_start: 0.8188 (pttm) cc_final: 0.7826 (ptmt) outliers start: 117 outliers final: 84 residues processed: 816 average time/residue: 0.1986 time to fit residues: 268.3162 Evaluate side-chains 818 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 721 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 309 ASN Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 139 MET Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 349 optimal weight: 0.0030 chunk 254 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 370 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.133174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102003 restraints weight = 64948.181| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.67 r_work: 0.3256 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 35113 Z= 0.162 Angle : 0.975 70.371 47616 Z= 0.349 Chirality : 0.045 0.377 5191 Planarity : 0.005 0.080 6032 Dihedral : 8.858 162.684 4966 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 3.00 % Allowed : 22.13 % Favored : 74.86 % 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: -0.68 (0.13), residues: 4166 helix: 0.55 (0.12), residues: 1835 sheet: -1.31 (0.27), residues: 366 loop : -1.22 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 52 TYR 0.033 0.002 TYR q 124 PHE 0.032 0.002 PHE G 409 TRP 0.057 0.001 TRP q 89 HIS 0.008 0.001 HIS P 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (35072) covalent geometry : angle 0.68848 / 0.34 (47524) SS BOND : bond 0.00362 / 0.19 ( 4) SS BOND : angle 1.49921 / 0.77 ( 8) hydrogen bonds : bond 0.03722 / 2.40 ( 1334) hydrogen bonds : angle 4.84990 / 3.45 ( 3777) metal coordination : bond 0.02123 / 1.48 ( 37) metal coordination : angle 16.43914 / 12.77 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 742 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TRP cc_start: 0.7235 (t60) cc_final: 0.6532 (t60) REVERT: B 83 ASN cc_start: 0.8359 (m-40) cc_final: 0.8100 (m-40) REVERT: B 104 MET cc_start: 0.8162 (tpt) cc_final: 0.7942 (tpt) REVERT: C 76 GLN cc_start: 0.8519 (pt0) cc_final: 0.8114 (pt0) REVERT: C 168 GLU cc_start: 0.8422 (tt0) cc_final: 0.7898 (tt0) REVERT: D 95 LEU cc_start: 0.9020 (tp) cc_final: 0.8541 (tp) REVERT: D 463 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7723 (ptt90) REVERT: E 61 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7314 (mtm-85) REVERT: E 109 MET cc_start: 0.8807 (tpp) cc_final: 0.8434 (tpp) REVERT: E 120 MET cc_start: 0.8931 (mmm) cc_final: 0.8545 (ttt) REVERT: E 151 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8726 (mm) REVERT: E 152 GLN cc_start: 0.8709 (mt0) cc_final: 0.8436 (mt0) REVERT: E 167 LEU cc_start: 0.8328 (tp) cc_final: 0.7932 (tp) REVERT: E 192 TYR cc_start: 0.7242 (m-80) cc_final: 0.6004 (m-80) REVERT: F 53 LEU cc_start: 0.8778 (tt) cc_final: 0.8506 (tp) REVERT: F 75 TRP cc_start: 0.8712 (t60) cc_final: 0.8301 (t60) REVERT: F 102 MET cc_start: 0.7278 (ptm) cc_final: 0.6990 (ttp) REVERT: F 157 TYR cc_start: 0.6241 (t80) cc_final: 0.5775 (t80) REVERT: F 170 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: F 269 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7530 (tpm170) REVERT: F 337 MET cc_start: 0.8638 (mtp) cc_final: 0.8159 (mtm) REVERT: F 450 MET cc_start: 0.8125 (mmp) cc_final: 0.7508 (mmt) REVERT: G 37 ASP cc_start: 0.8521 (t0) cc_final: 0.8311 (t0) REVERT: G 145 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8484 (mmm) REVERT: G 172 ILE cc_start: 0.9091 (mt) cc_final: 0.8706 (mm) REVERT: G 197 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8559 (p) REVERT: G 295 ASP cc_start: 0.8338 (p0) cc_final: 0.8069 (p0) REVERT: G 304 GLU cc_start: 0.8381 (tt0) cc_final: 0.8054 (tt0) REVERT: G 316 TYR cc_start: 0.8352 (m-80) cc_final: 0.7113 (m-80) REVERT: G 324 SER cc_start: 0.9112 (m) cc_final: 0.8693 (p) REVERT: G 380 ASP cc_start: 0.7916 (m-30) cc_final: 0.7664 (m-30) REVERT: G 496 MET cc_start: 0.9069 (tpp) cc_final: 0.8853 (tpp) REVERT: G 530 TYR cc_start: 0.8703 (m-80) cc_final: 0.8138 (m-80) REVERT: G 660 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7807 (mm-30) REVERT: G 696 MET cc_start: 0.8596 (mtm) cc_final: 0.8352 (mtt) REVERT: H 31 MET cc_start: 0.8974 (mtt) cc_final: 0.8589 (mtp) REVERT: H 59 GLU cc_start: 0.8518 (tt0) cc_final: 0.8275 (tt0) REVERT: H 184 MET cc_start: 0.8614 (mtp) cc_final: 0.8340 (mtp) REVERT: H 253 GLU cc_start: 0.8212 (pm20) cc_final: 0.7968 (pp20) REVERT: H 274 ARG cc_start: 0.9173 (ttt90) cc_final: 0.8914 (ttm-80) REVERT: H 277 TYR cc_start: 0.9018 (m-80) cc_final: 0.8449 (m-80) REVERT: H 282 TYR cc_start: 0.8653 (t80) cc_final: 0.8437 (t80) REVERT: I 177 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9087 (p) REVERT: P 107 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8568 (mp0) REVERT: P 128 ASN cc_start: 0.8357 (t0) cc_final: 0.8065 (t0) REVERT: P 205 ASP cc_start: 0.8186 (m-30) cc_final: 0.7806 (t0) REVERT: P 210 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: P 214 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8323 (tp) REVERT: Q 73 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8853 (mtmm) REVERT: S 17 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7171 (mmt-90) REVERT: S 79 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7308 (pp) REVERT: S 89 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8038 (mtm180) REVERT: T 81 ASP cc_start: 0.8939 (t0) cc_final: 0.8504 (m-30) REVERT: T 90 TYR cc_start: 0.7843 (t80) cc_final: 0.7440 (t80) REVERT: T 143 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8397 (mp0) REVERT: V 34 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8429 (tp) REVERT: V 57 ASP cc_start: 0.8784 (m-30) cc_final: 0.8386 (m-30) REVERT: V 83 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8696 (tp40) REVERT: W 68 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8294 (tm-30) REVERT: W 99 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6770 (t) REVERT: W 102 GLN cc_start: 0.6864 (mm-40) cc_final: 0.6621 (mm-40) REVERT: X 55 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7727 (mtt-85) REVERT: X 113 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: Z 80 ASP cc_start: 0.8165 (m-30) cc_final: 0.7946 (m-30) REVERT: Z 103 ASN cc_start: 0.7908 (m-40) cc_final: 0.7572 (p0) REVERT: a 35 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7754 (mt-10) REVERT: a 55 SER cc_start: 0.7352 (m) cc_final: 0.7064 (p) REVERT: b 51 TYR cc_start: 0.8483 (m-10) cc_final: 0.7831 (m-10) REVERT: q 81 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5184 (mpp) REVERT: q 124 TYR cc_start: 0.7578 (t80) cc_final: 0.7314 (t80) REVERT: q 133 LYS cc_start: 0.8242 (pttm) cc_final: 0.7877 (ptmt) REVERT: r 11 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7320 (tt) outliers start: 110 outliers final: 82 residues processed: 799 average time/residue: 0.2125 time to fit residues: 281.0270 Evaluate side-chains 811 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 714 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 309 ASN Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 139 MET Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 53 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 360 optimal weight: 8.9990 chunk 252 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS F 116 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 HIS ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.131632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.100197 restraints weight = 65170.326| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.66 r_work: 0.3240 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 35113 Z= 0.199 Angle : 1.008 73.078 47616 Z= 0.364 Chirality : 0.047 0.450 5191 Planarity : 0.005 0.080 6032 Dihedral : 8.913 163.200 4966 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 3.08 % Allowed : 22.46 % Favored : 74.45 % 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: -0.72 (0.13), residues: 4166 helix: 0.52 (0.12), residues: 1845 sheet: -1.30 (0.27), residues: 364 loop : -1.25 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 117 TYR 0.031 0.002 TYR P 84 PHE 0.032 0.002 PHE G 409 TRP 0.069 0.001 TRP q 89 HIS 0.007 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (35072) covalent geometry : angle 0.71801 / 0.36 (47524) SS BOND : bond 0.00372 / 0.19 ( 4) SS BOND : angle 1.57046 / 0.82 ( 8) hydrogen bonds : bond 0.03857 / 2.49 ( 1334) hydrogen bonds : angle 4.88614 / 3.48 ( 3777) metal coordination : bond 0.02548 / 1.73 ( 37) metal coordination : angle 16.84425 / 13.04 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8332 Ramachandran restraints generated. 4166 Oldfield, 0 Emsley, 4166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 733 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TRP cc_start: 0.7385 (t60) cc_final: 0.6771 (t60) REVERT: B 83 ASN cc_start: 0.8443 (m-40) cc_final: 0.8190 (m-40) REVERT: B 104 MET cc_start: 0.8186 (tpt) cc_final: 0.7983 (tpt) REVERT: B 161 MET cc_start: 0.8929 (tpp) cc_final: 0.8651 (mmm) REVERT: B 170 TYR cc_start: 0.7717 (t80) cc_final: 0.6931 (t80) REVERT: B 211 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8564 (ttmt) REVERT: C 168 GLU cc_start: 0.8446 (tt0) cc_final: 0.7867 (tt0) REVERT: D 95 LEU cc_start: 0.8951 (tp) cc_final: 0.8452 (tp) REVERT: D 463 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7726 (ptt90) REVERT: E 109 MET cc_start: 0.8830 (tpp) cc_final: 0.8492 (tpp) REVERT: E 120 MET cc_start: 0.8936 (mmm) cc_final: 0.8542 (ttt) REVERT: E 151 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8815 (mm) REVERT: E 167 LEU cc_start: 0.8361 (tp) cc_final: 0.7962 (tp) REVERT: F 53 LEU cc_start: 0.8790 (tt) cc_final: 0.8511 (tp) REVERT: F 75 TRP cc_start: 0.8768 (t60) cc_final: 0.8291 (t60) REVERT: F 102 MET cc_start: 0.7310 (ptm) cc_final: 0.7019 (ttp) REVERT: F 170 GLN cc_start: 0.8459 (tt0) cc_final: 0.7962 (tm-30) REVERT: F 269 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7496 (tpm170) REVERT: F 337 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8126 (mtm) REVERT: G 145 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8080 (mtp) REVERT: G 197 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8618 (p) REVERT: G 295 ASP cc_start: 0.8446 (p0) cc_final: 0.8191 (p0) REVERT: G 304 GLU cc_start: 0.8416 (tt0) cc_final: 0.8064 (tt0) REVERT: G 316 TYR cc_start: 0.8347 (m-80) cc_final: 0.7084 (m-80) REVERT: G 324 SER cc_start: 0.9094 (m) cc_final: 0.8669 (p) REVERT: G 380 ASP cc_start: 0.7937 (m-30) cc_final: 0.7703 (m-30) REVERT: G 496 MET cc_start: 0.9093 (tpp) cc_final: 0.8889 (tpp) REVERT: G 660 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7875 (mm-30) REVERT: G 696 MET cc_start: 0.8685 (mtm) cc_final: 0.8445 (mtt) REVERT: H 31 MET cc_start: 0.9008 (mtt) cc_final: 0.8658 (mtp) REVERT: H 59 GLU cc_start: 0.8534 (tt0) cc_final: 0.8282 (tt0) REVERT: H 184 MET cc_start: 0.8653 (mtp) cc_final: 0.8391 (mtp) REVERT: H 253 GLU cc_start: 0.8307 (pm20) cc_final: 0.8068 (pp20) REVERT: H 277 TYR cc_start: 0.9003 (m-80) cc_final: 0.8406 (m-80) REVERT: H 282 TYR cc_start: 0.8780 (t80) cc_final: 0.8513 (t80) REVERT: I 55 ASP cc_start: 0.8579 (m-30) cc_final: 0.8114 (m-30) REVERT: I 89 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7903 (mt-10) REVERT: P 107 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8517 (mp0) REVERT: P 128 ASN cc_start: 0.8389 (t0) cc_final: 0.8129 (t0) REVERT: P 210 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: P 214 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8295 (tp) REVERT: P 257 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6393 (p0) REVERT: Q 73 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8870 (mtmm) REVERT: Q 93 ASN cc_start: 0.9009 (m-40) cc_final: 0.8759 (m110) REVERT: Q 149 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8552 (mm-30) REVERT: S 17 ARG cc_start: 0.7673 (mmm160) cc_final: 0.7252 (mmt-90) REVERT: S 79 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7284 (pp) REVERT: T 81 ASP cc_start: 0.8921 (t0) cc_final: 0.8617 (m-30) REVERT: T 90 TYR cc_start: 0.7936 (t80) cc_final: 0.7157 (t80) REVERT: T 143 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8461 (mp0) REVERT: V 34 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8446 (tp) REVERT: V 57 ASP cc_start: 0.8771 (m-30) cc_final: 0.8369 (m-30) REVERT: V 83 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8726 (tp40) REVERT: W 68 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8284 (tm-30) REVERT: W 99 VAL cc_start: 0.7090 (OUTLIER) cc_final: 0.6841 (t) REVERT: W 102 GLN cc_start: 0.6881 (mm-40) cc_final: 0.6554 (mm-40) REVERT: X 55 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7681 (mtt-85) REVERT: X 113 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: Z 103 ASN cc_start: 0.7909 (m-40) cc_final: 0.7602 (p0) REVERT: a 35 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7762 (mt-10) REVERT: b 51 TYR cc_start: 0.8514 (m-10) cc_final: 0.7839 (m-10) REVERT: b 74 LEU cc_start: 0.8832 (mp) cc_final: 0.8624 (tp) REVERT: q 81 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.5274 (mpp) REVERT: q 124 TYR cc_start: 0.7610 (t80) cc_final: 0.7224 (t80) REVERT: q 133 LYS cc_start: 0.8272 (pttm) cc_final: 0.7806 (ptmt) REVERT: r 11 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7316 (tt) outliers start: 113 outliers final: 89 residues processed: 786 average time/residue: 0.2198 time to fit residues: 285.5562 Evaluate side-chains 816 residues out of total 3664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 711 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 309 ASN Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 71 ASN Chi-restraints excluded: chain P residue 76 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 117 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 139 MET Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 29 ASN Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 113 ASP Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 16 TYR Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 247 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 321 optimal weight: 10.0000 chunk 51 optimal weight: 0.0050 chunk 112 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 GLN W 61 GLN a 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.135169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104370 restraints weight = 65504.771| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.83 r_work: 0.3262 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 35113 Z= 0.143 Angle : 0.976 71.190 47616 Z= 0.348 Chirality : 0.045 0.335 5191 Planarity : 0.005 0.081 6032 Dihedral : 8.817 163.869 4966 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 2.78 % Allowed : 22.82 % Favored : 74.40 % 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: -0.65 (0.13), residues: 4166 helix: 0.59 (0.12), residues: 1843 sheet: -1.31 (0.27), residues: 364 loop : -1.21 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 87 TYR 0.031 0.002 TYR P 84 PHE 0.024 0.001 PHE Q 164 TRP 0.062 0.001 TRP q 89 HIS 0.009 0.001 HIS P 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (35072) covalent geometry : angle 0.68936 / 0.34 (47524) SS BOND : bond 0.00364 / 0.19 ( 4) SS BOND : angle 1.40896 / 0.72 ( 8) hydrogen bonds : bond 0.03681 / 2.38 ( 1334) hydrogen bonds : angle 4.78190 / 3.41 ( 3777) metal coordination : bond 0.01775 / 1.24 ( 37) metal coordination : angle 16.46375 / 12.86 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9463.67 seconds wall clock time: 162 minutes 39.78 seconds (9759.78 seconds total)