Starting phenix.real_space_refine on Tue May 5 22:42:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnz_38520/05_2026/8xnz_38520_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnz_38520/05_2026/8xnz_38520.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/8xnz_38520/05_2026/8xnz_38520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnz_38520/05_2026/8xnz_38520.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnz_38520/05_2026/8xnz_38520_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnz_38520/05_2026/8xnz_38520_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= 0.004 sd= 0.094 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 11 5.49 5 S 246 5.16 5 C 21816 2.51 5 N 5791 2.21 5 O 6197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34090 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 901 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 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: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3273 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 21, 'TRANS': 402} 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: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2531 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 22, 'TRANS': 294} Chain breaks: 1 Chain: "I" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1389 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} 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: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1153 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 11, 'TRANS': 67} Chain: "q" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1020 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 9, 'TRANS': 112} Chain breaks: 1 Chain: "r" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 418 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Chain: "s" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PC1': 1, 'SF4': 1, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-3': 1, 'UQ9:plan-4': 1, 'UQ9:plan-5': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 37 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'3PE': 2, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1153 SG CYS B 99 79.093 62.173 106.562 1.00 29.52 S ATOM 1656 SG CYS B 164 76.980 57.288 111.066 1.00 28.96 S ATOM 1886 SG CYS B 194 82.139 57.361 110.338 1.00 29.28 S ATOM 1159 SG CYS B 100 78.484 57.481 104.784 1.00 30.11 S ATOM 7666 SG CYS E 134 139.116 53.496 153.039 1.00 56.01 S ATOM 7700 SG CYS E 139 141.946 54.753 152.747 1.00 56.50 S ATOM 8007 SG CYS E 179 140.206 58.812 156.338 1.00 57.95 S ATOM 11161 SG CYS F 379 118.095 56.397 155.236 1.00 43.09 S ATOM 11180 SG CYS F 382 115.902 60.655 151.756 1.00 40.29 S ATOM 11200 SG CYS F 385 120.342 59.524 150.213 1.00 39.95 S ATOM 11522 SG CYS F 425 120.153 61.837 156.071 1.00 45.60 S ATOM 12570 SG CYS G 131 100.384 49.106 138.446 1.00 31.31 S ATOM 12549 SG CYS G 128 102.300 53.152 133.985 1.00 30.26 S ATOM 12610 SG CYS G 137 99.818 54.950 140.035 1.00 33.13 S ATOM 13295 SG CYS G 226 101.824 48.915 147.048 1.00 34.31 S ATOM 12966 SG CYS G 182 104.967 47.187 152.785 1.00 36.31 S ATOM 12942 SG CYS G 179 104.167 52.812 150.400 1.00 35.62 S ATOM 12919 SG CYS G 176 107.792 48.750 147.847 1.00 34.05 S ATOM 12056 SG CYS G 64 105.219 59.302 153.696 1.00 35.53 S ATOM 12142 SG CYS G 75 105.896 60.684 150.958 1.00 36.47 S ATOM 12167 SG CYS G 78 104.922 65.080 153.051 1.00 36.76 S ATOM 12268 SG CYS G 92 104.522 63.291 156.358 1.00 39.04 S ATOM 20280 SG CYS I 123 85.335 52.255 119.998 1.00 27.30 S ATOM 20506 SG CYS I 152 85.888 51.176 113.585 1.00 27.39 S ATOM 20553 SG CYS I 158 91.642 51.535 116.454 1.00 26.60 S ATOM 20532 SG CYS I 155 88.792 56.273 116.379 1.00 27.04 S ATOM 20229 SG CYS I 116 96.032 48.350 126.822 1.00 29.24 S ATOM 20252 SG CYS I 119 92.034 47.927 123.051 1.00 28.85 S ATOM 20210 SG CYS I 113 95.130 43.275 123.386 1.00 28.61 S ATOM 20582 SG CYS I 162 97.876 48.047 121.469 1.00 28.07 S ATOM 25081 SG CYS R 79 111.746 41.573 126.111 1.00 32.60 S ATOM 25257 SG CYS R 104 109.320 40.021 127.476 1.00 32.49 S ATOM 25279 SG CYS R 107 108.689 40.727 124.053 1.00 30.78 S Time building chain proxies: 7.55, per 1000 atoms: 0.22 Number of scatterers: 34090 At special positions: 0 Unit cell: (166, 129.48, 203.35, 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 246 16.00 P 11 15.00 O 6197 8.00 N 5791 7.00 C 21816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.04 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 969.5 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 302 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE1 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 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7878 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 35 sheets defined 50.1% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 83 through 108 Processing helix chain 'B' and resid 70 through 89 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.591A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.604A 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: 4.319A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.115A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.967A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.297A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.772A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.862A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.705A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 3.691A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.670A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.530A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.618A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.526A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 143 through 156 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 84 removed outlier: 3.601A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Proline residue: F 73 - end of helix Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.234A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.650A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.845A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.710A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.832A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 258 removed outlier: 3.600A 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 265 removed outlier: 3.919A pdb=" N PHE F 262 " --> pdb=" O GLY F 258 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 Processing helix chain 'F' and resid 328 through 335 removed outlier: 4.062A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.545A 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: 3.647A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.349A 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 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 140 through 147 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.931A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.818A 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 297 No H-bonds generated for 'chain 'G' and resid 295 through 297' Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 395 removed outlier: 4.192A pdb=" N GLU G 395 " --> pdb=" O ILE G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.024A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 458 removed outlier: 4.286A pdb=" N GLN G 453 " --> pdb=" O PRO G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 469 removed outlier: 4.114A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.634A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.524A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.641A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.749A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.573A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 86 Proline residue: H 75 - end of helix removed outlier: 3.624A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 124 removed outlier: 4.464A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.553A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.736A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 203 removed outlier: 3.908A pdb=" N GLY H 203 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 213 removed outlier: 3.547A pdb=" N VAL H 213 " --> pdb=" O GLY H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.931A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 63 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.619A pdb=" N GLY I 69 " --> pdb=" O GLU I 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.865A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.146A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.783A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.901A pdb=" N HIS P 93 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.106A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 removed outlier: 3.625A pdb=" N ALA P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.623A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 219 removed outlier: 4.163A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA P 218 " --> pdb=" O LEU P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 223 Processing helix chain 'P' and resid 229 through 233 Processing helix chain 'P' and resid 242 through 255 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.622A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 335 through 339 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.033A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 360 through 364 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.413A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 4.201A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'R' and resid 44 through 49 Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.550A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 59 through 64' Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 6.446A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 removed outlier: 3.810A pdb=" N TYR T 90 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 127 Processing helix chain 'T' and resid 133 through 138 removed outlier: 3.624A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.677A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.585A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 removed outlier: 3.931A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 98 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 128 Processing helix chain 'X' and resid 9 through 14 removed outlier: 3.563A pdb=" N LEU X 13 " --> pdb=" O THR X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.622A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 52 through 77 removed outlier: 4.542A pdb=" N CYS X 56 " --> pdb=" O ASP X 52 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS X 58 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU X 59 " --> pdb=" O ARG X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.945A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix removed outlier: 3.906A pdb=" N MET Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.500A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.633A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR a 30 " --> pdb=" O ILE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.760A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.603A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 78 through 82 removed outlier: 3.537A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.127A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 17 Processing helix chain 's' and resid 43 through 53 Processing helix chain 's' and resid 54 through 56 No H-bonds generated for 'chain 's' and resid 54 through 56' Processing sheet with id=AA1, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.066A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 74 removed outlier: 3.522A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 117 removed outlier: 6.047A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.149A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.564A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.616A pdb=" N MET D 80 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N HIS D 442 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.309A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 397 through 401 Processing sheet with id=AB1, first strand: chain 'E' and resid 171 through 173 removed outlier: 3.701A pdb=" N CYS E 134 " --> pdb=" O MET E 184 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N MET E 184 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 194 through 199 removed outlier: 7.393A pdb=" N ARG F 152 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE F 196 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LYS F 111 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N TYR F 155 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 286 through 287 removed outlier: 6.348A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 294 through 295 removed outlier: 4.076A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 34 removed outlier: 3.730A pdb=" N VAL G 34 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 89 through 90 Processing sheet with id=AB7, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'G' and resid 246 through 251 removed outlier: 8.153A pdb=" N ASN G 260 " --> pdb=" O PRO G 275 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL G 262 " --> pdb=" O ILE G 273 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE G 273 " --> pdb=" O VAL G 262 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER G 264 " --> pdb=" O MET G 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 299 through 301 removed outlier: 5.943A pdb=" N HIS q 135 " --> pdb=" O ARG G 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 307 through 308 Processing sheet with id=AC2, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.093A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA G 339 " --> pdb=" O PHE G 546 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU G 548 " --> pdb=" O ALA G 339 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE G 341 " --> pdb=" O LEU G 548 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.204A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC6, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.409A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.225A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL P 126 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL P 167 " --> pdb=" O VAL P 126 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASN P 128 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE P 200 " --> pdb=" O PHE P 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 205 through 207 removed outlier: 6.218A pdb=" N ASP P 205 " --> pdb=" O VAL P 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'P' and resid 226 through 227 removed outlier: 5.711A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'P' and resid 236 through 237 Processing sheet with id=AD2, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AD3, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'R' and resid 76 through 79 removed outlier: 4.032A pdb=" N VAL R 91 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing sheet with id=AD5, 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=AD6, first strand: chain 'S' and resid 53 through 56 removed outlier: 3.671A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD8, first strand: chain 'q' and resid 37 through 42 removed outlier: 6.237A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) 1439 hydrogen bonds defined for protein. 4158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.35: 11026 1.35 - 1.57: 23389 1.57 - 1.79: 207 1.79 - 2.02: 206 2.02 - 2.24: 80 Bond restraints: 34908 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=" C ALA E 227 " pdb=" O ALA E 227 " ideal model delta sigma weight residual 1.236 1.419 -0.184 1.16e-02 7.43e+03 2.50e+02 bond pdb=" N PRO R 89 " pdb=" CD PRO R 89 " ideal model delta sigma weight residual 1.473 1.261 0.212 1.40e-02 5.10e+03 2.29e+02 bond pdb=" N PRO q 139 " pdb=" CD PRO q 139 " ideal model delta sigma weight residual 1.473 1.283 0.190 1.40e-02 5.10e+03 1.85e+02 bond pdb=" N PRO P 371 " pdb=" CD PRO P 371 " ideal model delta sigma weight residual 1.473 1.654 -0.181 1.40e-02 5.10e+03 1.67e+02 ... (remaining 34903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.68: 46596 6.68 - 13.36: 538 13.36 - 20.03: 169 20.03 - 26.71: 4 26.71 - 33.39: 2 Bond angle restraints: 47309 Sorted by residual: angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" CB VAL D 142 " ideal model delta sigma weight residual 110.65 132.41 -21.76 1.13e+00 7.83e-01 3.71e+02 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 110.42 92.49 17.93 9.40e-01 1.13e+00 3.64e+02 angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.39 89.08 25.31 1.45e+00 4.76e-01 3.05e+02 angle pdb=" N CYS F 332 " pdb=" CA CYS F 332 " pdb=" C CYS F 332 " ideal model delta sigma weight residual 111.02 130.00 -18.98 1.22e+00 6.72e-01 2.42e+02 angle pdb=" N GLU r 91 " pdb=" CA GLU r 91 " pdb=" CB GLU r 91 " ideal model delta sigma weight residual 110.50 135.23 -24.73 1.70e+00 3.46e-01 2.12e+02 ... (remaining 47304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 20688 35.35 - 70.70: 346 70.70 - 106.04: 31 106.04 - 141.39: 7 141.39 - 176.74: 2 Dihedral angle restraints: 21074 sinusoidal: 8852 harmonic: 12222 Sorted by residual: dihedral pdb=" N GLU r 91 " pdb=" C GLU r 91 " pdb=" CA GLU r 91 " pdb=" CB GLU r 91 " ideal model delta harmonic sigma weight residual 122.80 167.11 -44.31 0 2.50e+00 1.60e-01 3.14e+02 dihedral pdb=" C GLU r 91 " pdb=" N GLU r 91 " pdb=" CA GLU r 91 " pdb=" CB GLU r 91 " ideal model delta harmonic sigma weight residual -122.60 -162.67 40.07 0 2.50e+00 1.60e-01 2.57e+02 dihedral pdb=" C ASP D 140 " pdb=" N ASP D 140 " pdb=" CA ASP D 140 " pdb=" CB ASP D 140 " ideal model delta harmonic sigma weight residual -122.60 -101.18 -21.42 0 2.50e+00 1.60e-01 7.34e+01 ... (remaining 21071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 5089 0.348 - 0.696: 56 0.696 - 1.044: 24 1.044 - 1.391: 0 1.391 - 1.739: 1 Chirality restraints: 5170 Sorted by residual: chirality pdb=" CA GLU r 91 " pdb=" N GLU r 91 " pdb=" C GLU r 91 " pdb=" CB GLU r 91 " both_signs ideal model delta sigma weight residual False 2.51 0.77 1.74 2.00e-01 2.50e+01 7.56e+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 2.09e+01 chirality pdb="FE4 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 5167 not shown) Planarity restraints: 6011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 B 302 " 0.066 2.00e-02 2.50e+03 2.62e-01 2.07e+03 pdb=" C1M UQ9 B 302 " 0.270 2.00e-02 2.50e+03 pdb=" C2 UQ9 B 302 " 0.028 2.00e-02 2.50e+03 pdb=" C3 UQ9 B 302 " -0.139 2.00e-02 2.50e+03 pdb=" C4 UQ9 B 302 " 0.138 2.00e-02 2.50e+03 pdb=" C5 UQ9 B 302 " -0.039 2.00e-02 2.50e+03 pdb=" C6 UQ9 B 302 " -0.077 2.00e-02 2.50e+03 pdb=" C7 UQ9 B 302 " -0.243 2.00e-02 2.50e+03 pdb=" O2 UQ9 B 302 " 0.130 2.00e-02 2.50e+03 pdb=" O3 UQ9 B 302 " -0.536 2.00e-02 2.50e+03 pdb=" O4 UQ9 B 302 " 0.561 2.00e-02 2.50e+03 pdb=" O5 UQ9 B 302 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 B 302 " -0.153 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C11 UQ9 B 302 " -0.118 2.00e-02 2.50e+03 pdb=" C7 UQ9 B 302 " -0.340 2.00e-02 2.50e+03 pdb=" C8 UQ9 B 302 " 0.509 2.00e-02 2.50e+03 pdb=" C9 UQ9 B 302 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ9 H 401 " -0.255 2.00e-02 2.50e+03 2.16e-01 5.81e+02 pdb=" C18 UQ9 H 401 " 0.362 2.00e-02 2.50e+03 pdb=" C19 UQ9 H 401 " 0.078 2.00e-02 2.50e+03 pdb=" C20 UQ9 H 401 " -0.010 2.00e-02 2.50e+03 pdb=" C21 UQ9 H 401 " -0.175 2.00e-02 2.50e+03 ... (remaining 6008 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 47 2.34 - 2.98: 21265 2.98 - 3.62: 53085 3.62 - 4.26: 85261 4.26 - 4.90: 138328 Nonbonded interactions: 297986 Sorted by model distance: nonbonded pdb=" O ASN F 270 " pdb=" OD1 ASN F 270 " model vdw 1.703 3.040 nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.755 3.040 nonbonded pdb=" O ASP q 76 " pdb=" OD1 ASP q 76 " model vdw 1.903 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASN P 376 " pdb=" N TYR P 377 " model vdw 1.980 3.120 ... (remaining 297981 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: 11.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.130 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.021 1.140 34949 Z= 1.071 Angle : 2.181 41.432 47399 Z= 1.460 Chirality : 0.126 1.739 5170 Planarity : 0.009 0.291 6011 Dihedral : 13.284 176.741 13187 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 42.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.60 % Favored : 94.38 % Rotamer: Outliers : 0.25 % Allowed : 7.12 % Favored : 92.63 % Cbeta Deviations : 1.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.12), residues: 4160 helix: -0.72 (0.11), residues: 1802 sheet: -1.09 (0.30), residues: 313 loop : -2.11 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 333 TYR 0.047 0.003 TYR B 112 PHE 0.051 0.002 PHE a 3 TRP 0.035 0.002 TRP G 285 HIS 0.012 0.002 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.01466 (34908) covalent geometry : angle 2.06732 (47309) SS BOND : bond 0.00792 ( 3) SS BOND : angle 2.23091 ( 6) hydrogen bonds : bond 0.24063 ( 1439) hydrogen bonds : angle 8.88857 ( 4158) metal coordination : bond 0.45796 ( 37) metal coordination : angle 16.65791 ( 84) Misc. bond : bond 0.59963 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1653 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1644 time to evaluate : 1.078 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: B 160 SER cc_start: 0.9145 (t) cc_final: 0.8921 (m) REVERT: C 58 SER cc_start: 0.8416 (t) cc_final: 0.7567 (p) REVERT: D 98 VAL cc_start: 0.8957 (p) cc_final: 0.8498 (t) REVERT: E 46 ASN cc_start: 0.7281 (t0) cc_final: 0.6955 (t0) REVERT: E 132 GLN cc_start: 0.8035 (mt0) cc_final: 0.7708 (mt0) REVERT: E 190 ASN cc_start: 0.7249 (m-40) cc_final: 0.6973 (m-40) REVERT: F 127 ASP cc_start: 0.7591 (m-30) cc_final: 0.7296 (m-30) REVERT: F 390 ASP cc_start: 0.7234 (t0) cc_final: 0.6710 (t0) REVERT: G 254 MET cc_start: 0.9079 (mmp) cc_final: 0.8785 (mmt) REVERT: H 72 ILE cc_start: 0.8844 (pp) cc_final: 0.8218 (mt) REVERT: H 291 LYS cc_start: 0.7821 (tppt) cc_final: 0.7572 (tptt) REVERT: P 114 ASP cc_start: 0.5732 (t0) cc_final: 0.4918 (t0) REVERT: T 86 VAL cc_start: 0.8232 (t) cc_final: 0.7894 (t) REVERT: T 130 ILE cc_start: 0.7257 (mp) cc_final: 0.6898 (mp) REVERT: T 142 GLN cc_start: 0.7697 (tp40) cc_final: 0.7448 (tp-100) REVERT: a 7 PRO cc_start: 0.8559 (Cg_exo) cc_final: 0.8245 (Cg_endo) outliers start: 9 outliers final: 3 residues processed: 1650 average time/residue: 0.2380 time to fit residues: 605.8356 Evaluate side-chains 899 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 896 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain T residue 103 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 26 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 195 HIS D 117 HIS D 131 GLN D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 381 HIS ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 270 ASN F 284 HIS F 376 HIS G 140 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN G 424 HIS G 444 HIS G 453 GLN ** G 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 235 ASN H 292 ASN I 126 GLN I 159 GLN P 171 ASN P 216 HIS P 219 ASN P 356 HIS Q 86 ASN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 ASN S 73 GLN S 81 ASN V 21 HIS V 50 GLN W 75 HIS W 105 HIS X 30 HIS X 40 ASN X 95 GLN X 104 GLN Z 76 GLN a 58 ASN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 31 ASN q 54 GLN r 21 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.099052 restraints weight = 73507.863| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.62 r_work: 0.3275 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 34949 Z= 0.195 Angle : 0.940 45.477 47399 Z= 0.410 Chirality : 0.048 0.229 5170 Planarity : 0.006 0.070 6011 Dihedral : 10.706 177.605 4903 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.89 % Allowed : 16.08 % Favored : 80.03 % 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: -0.77 (0.13), residues: 4160 helix: 0.48 (0.12), residues: 1881 sheet: -1.11 (0.27), residues: 345 loop : -1.37 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG P 117 TYR 0.031 0.002 TYR W 43 PHE 0.034 0.002 PHE D 458 TRP 0.026 0.002 TRP b 80 HIS 0.009 0.002 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00432 (34908) covalent geometry : angle 0.79036 (47309) SS BOND : bond 0.01255 ( 3) SS BOND : angle 1.79139 ( 6) hydrogen bonds : bond 0.05892 ( 1439) hydrogen bonds : angle 5.64291 ( 4158) metal coordination : bond 0.02844 ( 37) metal coordination : angle 12.08681 ( 84) Misc. bond : bond 0.00138 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 994 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.6491 (t80) cc_final: 0.6232 (t80) REVERT: B 122 ARG cc_start: 0.7853 (mmp-170) cc_final: 0.7269 (mmm160) REVERT: B 141 MET cc_start: 0.9057 (tpp) cc_final: 0.8734 (tpp) REVERT: C 58 SER cc_start: 0.8420 (t) cc_final: 0.7679 (p) REVERT: D 185 MET cc_start: 0.8559 (tpp) cc_final: 0.7838 (tpp) REVERT: E 41 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7402 (mtt180) REVERT: E 46 ASN cc_start: 0.7712 (t0) cc_final: 0.6492 (t0) REVERT: E 54 PHE cc_start: 0.8520 (m-80) cc_final: 0.8178 (m-80) REVERT: E 132 GLN cc_start: 0.9097 (mt0) cc_final: 0.8778 (mt0) REVERT: E 218 ARG cc_start: 0.6989 (mmm160) cc_final: 0.6758 (ttt90) REVERT: F 63 TYR cc_start: 0.8459 (t80) cc_final: 0.8218 (t80) REVERT: F 225 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8709 (mp) REVERT: G 32 ILE cc_start: 0.8473 (mm) cc_final: 0.8272 (mm) REVERT: G 77 MET cc_start: 0.9038 (tpt) cc_final: 0.8701 (tpt) REVERT: G 202 ASN cc_start: 0.8002 (m-40) cc_final: 0.7578 (m110) REVERT: G 213 MET cc_start: 0.8013 (ptm) cc_final: 0.7581 (ptm) REVERT: G 558 GLN cc_start: 0.8066 (tt0) cc_final: 0.7154 (tp40) REVERT: H 53 MET cc_start: 0.8857 (mtt) cc_final: 0.8579 (mtp) REVERT: H 72 ILE cc_start: 0.9033 (pp) cc_final: 0.8622 (mt) REVERT: H 159 SER cc_start: 0.8600 (t) cc_final: 0.8324 (p) REVERT: H 172 MET cc_start: 0.8091 (ppp) cc_final: 0.7756 (ppp) REVERT: H 291 LYS cc_start: 0.8771 (tppt) cc_final: 0.7676 (tppt) REVERT: I 59 ARG cc_start: 0.7939 (ttp-110) cc_final: 0.7731 (ttp-110) REVERT: I 159 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8447 (mt0) REVERT: P 72 HIS cc_start: 0.8597 (m90) cc_final: 0.8301 (m-70) REVERT: P 154 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8343 (tp40) REVERT: P 188 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7828 (mt-10) REVERT: P 217 PHE cc_start: 0.8691 (m-10) cc_final: 0.8345 (m-10) REVERT: P 271 TYR cc_start: 0.7867 (m-80) cc_final: 0.7642 (m-80) REVERT: P 324 ILE cc_start: 0.8566 (mm) cc_final: 0.8148 (mt) REVERT: P 353 LEU cc_start: 0.8819 (mt) cc_final: 0.8570 (mt) REVERT: Q 86 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.7934 (t0) REVERT: R 67 GLN cc_start: 0.8109 (tp40) cc_final: 0.7720 (tp40) REVERT: S 57 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7765 (mt-10) REVERT: S 62 GLN cc_start: 0.8401 (pt0) cc_final: 0.8148 (pt0) REVERT: S 64 LYS cc_start: 0.6777 (mtmm) cc_final: 0.6429 (pttm) REVERT: S 82 LEU cc_start: 0.8904 (mt) cc_final: 0.8698 (mt) REVERT: T 97 LYS cc_start: 0.7388 (tptp) cc_final: 0.7173 (mmmm) REVERT: T 114 ASP cc_start: 0.8108 (t0) cc_final: 0.7645 (t0) REVERT: T 117 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7368 (mt-10) REVERT: T 120 MET cc_start: 0.7961 (mtp) cc_final: 0.7555 (mtp) REVERT: T 122 MET cc_start: 0.8082 (mmt) cc_final: 0.7779 (mmp) REVERT: T 133 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7295 (tp) REVERT: T 142 GLN cc_start: 0.8529 (tp40) cc_final: 0.8253 (tp-100) REVERT: V 64 ASP cc_start: 0.7413 (t0) cc_final: 0.7173 (t70) REVERT: V 65 VAL cc_start: 0.7703 (p) cc_final: 0.7479 (p) REVERT: V 107 PRO cc_start: 0.8707 (Cg_endo) cc_final: 0.8389 (Cg_exo) REVERT: W 30 GLU cc_start: 0.8647 (tt0) cc_final: 0.8248 (mt-10) REVERT: W 53 MET cc_start: 0.8608 (mtt) cc_final: 0.8294 (mtt) REVERT: W 92 GLU cc_start: 0.8893 (tp30) cc_final: 0.8684 (tp30) REVERT: W 104 THR cc_start: 0.8875 (p) cc_final: 0.8649 (t) REVERT: W 124 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8014 (mtmm) REVERT: X 40 ASN cc_start: 0.8311 (m-40) cc_final: 0.8065 (m110) REVERT: X 52 ASP cc_start: 0.6535 (p0) cc_final: 0.6296 (p0) REVERT: Z 76 GLN cc_start: 0.9014 (tp40) cc_final: 0.8627 (tp40) REVERT: Z 133 MET cc_start: 0.8425 (tmm) cc_final: 0.7914 (tpp) REVERT: Z 142 TRP cc_start: 0.7236 (m-10) cc_final: 0.7006 (m-10) REVERT: a 61 TYR cc_start: 0.6795 (m-80) cc_final: 0.6214 (m-80) REVERT: b 16 GLU cc_start: 0.7750 (mp0) cc_final: 0.7490 (pt0) REVERT: b 47 LYS cc_start: 0.8315 (tmmt) cc_final: 0.7945 (tttt) REVERT: s 67 PRO cc_start: 0.4478 (Cg_exo) cc_final: 0.4095 (Cg_endo) outliers start: 142 outliers final: 66 residues processed: 1068 average time/residue: 0.2108 time to fit residues: 367.4826 Evaluate side-chains 874 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 803 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 467 LYS Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 527 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 118 ILE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain X residue 142 TYR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 278 optimal weight: 0.9990 chunk 384 optimal weight: 5.9990 chunk 400 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 380 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 130 ASN C 180 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 HIS ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 455 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** G 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN I 159 GLN P 166 HIS P 216 HIS P 238 GLN Q 86 ASN Q 109 ASN ** R 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 73 GLN V 50 GLN ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 69 ASN X 104 GLN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.118510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096265 restraints weight = 73288.511| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.59 r_work: 0.3229 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 34949 Z= 0.171 Angle : 0.856 59.594 47399 Z= 0.354 Chirality : 0.045 0.241 5170 Planarity : 0.005 0.079 6011 Dihedral : 10.378 173.470 4901 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.70 % Allowed : 18.73 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4160 helix: 0.87 (0.12), residues: 1880 sheet: -1.06 (0.27), residues: 346 loop : -1.04 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 89 TYR 0.025 0.002 TYR V 44 PHE 0.021 0.002 PHE H 310 TRP 0.021 0.001 TRP Q 166 HIS 0.008 0.001 HIS F 284 Details of bonding type rmsd covalent geometry : bond 0.00396 (34908) covalent geometry : angle 0.68997 (47309) SS BOND : bond 0.00466 ( 3) SS BOND : angle 1.50949 ( 6) hydrogen bonds : bond 0.04876 ( 1439) hydrogen bonds : angle 5.17222 ( 4158) metal coordination : bond 0.02269 ( 37) metal coordination : angle 12.05438 ( 84) Misc. bond : bond 0.00136 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 868 time to evaluate : 0.894 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 51 PHE cc_start: 0.6277 (t80) cc_final: 0.6055 (t80) REVERT: C 58 SER cc_start: 0.8309 (t) cc_final: 0.7721 (p) REVERT: D 185 MET cc_start: 0.8595 (tpp) cc_final: 0.7875 (tpp) REVERT: D 443 MET cc_start: 0.8523 (mpp) cc_final: 0.8284 (mpp) REVERT: E 46 ASN cc_start: 0.7481 (t0) cc_final: 0.6539 (t0) REVERT: E 87 ARG cc_start: 0.8912 (mmt180) cc_final: 0.8661 (mmt90) REVERT: E 153 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7790 (ttm110) REVERT: F 217 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7576 (tt0) REVERT: F 225 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8971 (mp) REVERT: F 246 GLU cc_start: 0.8676 (tt0) cc_final: 0.8341 (tt0) REVERT: G 32 ILE cc_start: 0.8611 (mm) cc_final: 0.8334 (mp) REVERT: G 42 MET cc_start: 0.8736 (tpp) cc_final: 0.8522 (tpp) REVERT: G 77 MET cc_start: 0.9029 (tpt) cc_final: 0.8604 (tpt) REVERT: G 114 GLU cc_start: 0.8156 (tt0) cc_final: 0.7555 (tm-30) REVERT: G 202 ASN cc_start: 0.7919 (m110) cc_final: 0.7615 (m110) REVERT: G 213 MET cc_start: 0.8036 (ptm) cc_final: 0.7710 (ptm) REVERT: G 254 MET cc_start: 0.9353 (mmt) cc_final: 0.9153 (mmm) REVERT: G 370 GLU cc_start: 0.8366 (tp30) cc_final: 0.7948 (mm-30) REVERT: G 558 GLN cc_start: 0.7946 (tt0) cc_final: 0.7674 (mm-40) REVERT: G 574 ASP cc_start: 0.8288 (t0) cc_final: 0.7849 (t0) REVERT: G 581 ASP cc_start: 0.8802 (m-30) cc_final: 0.8340 (m-30) REVERT: G 628 GLU cc_start: 0.8680 (tp30) cc_final: 0.8416 (tp30) REVERT: H 53 MET cc_start: 0.8874 (mtt) cc_final: 0.8609 (mtp) REVERT: H 72 ILE cc_start: 0.8979 (pp) cc_final: 0.8678 (mt) REVERT: H 97 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8065 (t0) REVERT: H 100 LEU cc_start: 0.8995 (mt) cc_final: 0.8738 (mt) REVERT: H 183 MET cc_start: 0.8552 (mtt) cc_final: 0.8288 (mtp) REVERT: H 192 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7664 (mm-30) REVERT: H 214 GLU cc_start: 0.7506 (mp0) cc_final: 0.7201 (mp0) REVERT: H 291 LYS cc_start: 0.8941 (tppt) cc_final: 0.7804 (tppt) REVERT: P 154 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8305 (tp-100) REVERT: P 271 TYR cc_start: 0.7977 (m-80) cc_final: 0.7654 (m-80) REVERT: P 324 ILE cc_start: 0.8628 (mm) cc_final: 0.8382 (mt) REVERT: R 45 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7276 (mtm110) REVERT: R 67 GLN cc_start: 0.8285 (tp40) cc_final: 0.7978 (tp40) REVERT: S 64 LYS cc_start: 0.6885 (mtmm) cc_final: 0.6514 (pttm) REVERT: T 97 LYS cc_start: 0.7635 (tptp) cc_final: 0.7239 (mmmm) REVERT: T 114 ASP cc_start: 0.7983 (t0) cc_final: 0.7523 (t0) REVERT: T 117 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7585 (mt-10) REVERT: T 118 ILE cc_start: 0.8723 (mm) cc_final: 0.8497 (mm) REVERT: V 64 ASP cc_start: 0.7541 (t0) cc_final: 0.7280 (t70) REVERT: W 30 GLU cc_start: 0.8620 (tt0) cc_final: 0.8221 (mt-10) REVERT: W 43 TYR cc_start: 0.9004 (t80) cc_final: 0.8684 (t80) REVERT: W 53 MET cc_start: 0.8635 (mtt) cc_final: 0.8407 (mtt) REVERT: Z 21 TYR cc_start: 0.8234 (p90) cc_final: 0.8013 (p90) REVERT: Z 76 GLN cc_start: 0.9000 (tp40) cc_final: 0.8685 (tp40) REVERT: Z 133 MET cc_start: 0.8460 (tmm) cc_final: 0.7988 (tpp) REVERT: a 28 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8748 (ttmm) REVERT: a 61 TYR cc_start: 0.7167 (m-80) cc_final: 0.6467 (m-80) REVERT: b 47 LYS cc_start: 0.8419 (tmmt) cc_final: 0.7997 (ttpt) REVERT: b 59 ASP cc_start: 0.7719 (t0) cc_final: 0.7499 (m-30) REVERT: b 71 GLN cc_start: 0.8205 (tt0) cc_final: 0.7893 (mt0) REVERT: q 60 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6539 (mtt180) REVERT: r 92 LYS cc_start: 0.7644 (mmpt) cc_final: 0.7218 (mmtm) outliers start: 135 outliers final: 74 residues processed: 946 average time/residue: 0.2090 time to fit residues: 322.6402 Evaluate side-chains 834 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 758 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 149 GLU Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 105 GLU Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 362 optimal weight: 0.7980 chunk 369 optimal weight: 9.9990 chunk 382 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 354 optimal weight: 8.9990 chunk 386 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 455 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** G 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 569 GLN ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 663 ASN I 159 GLN P 72 HIS Q 86 ASN R 33 HIS S 39 GLN S 73 GLN V 50 GLN ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 ASN X 104 GLN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 ASN ** 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 = 0.3718 r_free = 0.3718 target = 0.119388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097372 restraints weight = 72973.259| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.56 r_work: 0.3244 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 34949 Z= 0.144 Angle : 0.822 65.690 47399 Z= 0.330 Chirality : 0.043 0.210 5170 Planarity : 0.005 0.054 6011 Dihedral : 9.958 158.388 4895 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.75 % Allowed : 19.83 % Favored : 76.42 % 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: -0.16 (0.13), residues: 4160 helix: 0.94 (0.12), residues: 1870 sheet: -1.19 (0.27), residues: 360 loop : -0.89 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 122 TYR 0.020 0.001 TYR G 236 PHE 0.025 0.002 PHE X 70 TRP 0.026 0.001 TRP Q 166 HIS 0.005 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00335 (34908) covalent geometry : angle 0.64576 (47309) SS BOND : bond 0.01628 ( 3) SS BOND : angle 2.58395 ( 6) hydrogen bonds : bond 0.04342 ( 1439) hydrogen bonds : angle 4.95410 ( 4158) metal coordination : bond 0.01622 ( 37) metal coordination : angle 12.08834 ( 84) Misc. bond : bond 0.00101 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 831 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.9028 (mm) cc_final: 0.8668 (mm) REVERT: B 122 ARG cc_start: 0.8361 (mmm160) cc_final: 0.7876 (mmm160) REVERT: D 185 MET cc_start: 0.8551 (tpp) cc_final: 0.7967 (tpp) REVERT: D 443 MET cc_start: 0.8546 (mpp) cc_final: 0.8250 (mpp) REVERT: E 46 ASN cc_start: 0.7374 (t0) cc_final: 0.6669 (t0) REVERT: E 132 GLN cc_start: 0.8867 (mt0) cc_final: 0.8067 (mt0) REVERT: E 184 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8148 (ptp) REVERT: E 194 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: F 217 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7617 (tt0) REVERT: F 246 GLU cc_start: 0.8637 (tt0) cc_final: 0.8392 (tt0) REVERT: F 390 ASP cc_start: 0.8323 (t0) cc_final: 0.7890 (m-30) REVERT: F 420 GLU cc_start: 0.7748 (tp30) cc_final: 0.7327 (tp30) REVERT: G 32 ILE cc_start: 0.8737 (mm) cc_final: 0.8482 (mp) REVERT: G 77 MET cc_start: 0.8981 (tpt) cc_final: 0.8561 (tpt) REVERT: G 114 GLU cc_start: 0.8164 (tt0) cc_final: 0.7612 (tm-30) REVERT: G 202 ASN cc_start: 0.7858 (m110) cc_final: 0.7161 (m-40) REVERT: G 205 GLN cc_start: 0.8666 (mt0) cc_final: 0.8348 (mp10) REVERT: G 254 MET cc_start: 0.9375 (mmt) cc_final: 0.9167 (mmm) REVERT: G 271 MET cc_start: 0.9142 (mmp) cc_final: 0.8914 (mmp) REVERT: G 315 THR cc_start: 0.9006 (m) cc_final: 0.8773 (p) REVERT: G 370 GLU cc_start: 0.8326 (tp30) cc_final: 0.7945 (mm-30) REVERT: G 513 MET cc_start: 0.8983 (tpp) cc_final: 0.8771 (tpp) REVERT: G 558 GLN cc_start: 0.7979 (tt0) cc_final: 0.7653 (mm-40) REVERT: G 574 ASP cc_start: 0.8048 (t0) cc_final: 0.7844 (t0) REVERT: G 581 ASP cc_start: 0.8827 (m-30) cc_final: 0.8369 (m-30) REVERT: G 628 GLU cc_start: 0.8686 (tp30) cc_final: 0.8407 (tp30) REVERT: H 47 GLN cc_start: 0.8899 (tp40) cc_final: 0.8620 (tp40) REVERT: H 53 MET cc_start: 0.8838 (mtt) cc_final: 0.8570 (mtp) REVERT: H 183 MET cc_start: 0.8550 (mtt) cc_final: 0.8331 (mtp) REVERT: H 192 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7527 (mm-30) REVERT: H 291 LYS cc_start: 0.9054 (tppt) cc_final: 0.7762 (tppt) REVERT: I 76 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7588 (t80) REVERT: I 208 ASP cc_start: 0.7864 (t0) cc_final: 0.7492 (t0) REVERT: P 140 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7234 (t0) REVERT: P 271 TYR cc_start: 0.8046 (m-80) cc_final: 0.7753 (m-80) REVERT: P 324 ILE cc_start: 0.8595 (mm) cc_final: 0.8343 (mp) REVERT: Q 88 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: R 45 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7494 (ttm170) REVERT: R 67 GLN cc_start: 0.8380 (tp40) cc_final: 0.8076 (tp40) REVERT: S 62 GLN cc_start: 0.8294 (pt0) cc_final: 0.7911 (pt0) REVERT: S 64 LYS cc_start: 0.6983 (mtmm) cc_final: 0.6475 (pttm) REVERT: S 66 TRP cc_start: 0.8644 (m100) cc_final: 0.8430 (m100) REVERT: S 82 LEU cc_start: 0.8766 (mt) cc_final: 0.8553 (mp) REVERT: T 97 LYS cc_start: 0.7736 (tptp) cc_final: 0.7271 (mmmm) REVERT: T 114 ASP cc_start: 0.8119 (t0) cc_final: 0.7671 (t0) REVERT: T 117 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7570 (mt-10) REVERT: T 118 ILE cc_start: 0.8712 (mm) cc_final: 0.8508 (mm) REVERT: T 139 MET cc_start: 0.7561 (tpp) cc_final: 0.6994 (tpp) REVERT: V 64 ASP cc_start: 0.7576 (t0) cc_final: 0.7367 (t70) REVERT: W 27 ASP cc_start: 0.8057 (p0) cc_final: 0.7812 (p0) REVERT: W 30 GLU cc_start: 0.8594 (tt0) cc_final: 0.8186 (mt-10) REVERT: W 43 TYR cc_start: 0.8984 (t80) cc_final: 0.8654 (t80) REVERT: X 37 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7709 (p0) REVERT: X 126 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7943 (m) REVERT: Z 10 MET cc_start: 0.8079 (mmm) cc_final: 0.7873 (mmm) REVERT: Z 21 TYR cc_start: 0.8269 (p90) cc_final: 0.8008 (p90) REVERT: Z 133 MET cc_start: 0.8511 (tmm) cc_final: 0.7813 (tpp) REVERT: a 28 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8689 (ttmm) REVERT: a 34 LYS cc_start: 0.8020 (ptpt) cc_final: 0.7750 (ptpt) REVERT: a 61 TYR cc_start: 0.7304 (m-80) cc_final: 0.6557 (m-80) REVERT: b 47 LYS cc_start: 0.8360 (tmmt) cc_final: 0.8108 (ttpt) REVERT: b 59 ASP cc_start: 0.7641 (t0) cc_final: 0.7396 (m-30) REVERT: b 71 GLN cc_start: 0.8206 (tt0) cc_final: 0.7916 (mt0) REVERT: q 124 TYR cc_start: 0.8017 (t80) cc_final: 0.7811 (t80) REVERT: r 92 LYS cc_start: 0.7721 (mmpt) cc_final: 0.7265 (mmtm) outliers start: 137 outliers final: 80 residues processed: 902 average time/residue: 0.2056 time to fit residues: 305.0078 Evaluate side-chains 845 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 758 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 289 GLU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 88 GLN Chi-restraints excluded: chain Q residue 149 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain T residue 146 ASP Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 104 GLN Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 28 ARG Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 376 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 197 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 361 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 455 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** G 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 235 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 ASN P 72 HIS S 73 GLN S 80 ASN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 129 HIS X 69 ASN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 ASN r 9 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.117813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095423 restraints weight = 73644.399| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.59 r_work: 0.3205 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34949 Z= 0.154 Angle : 0.819 69.256 47399 Z= 0.324 Chirality : 0.043 0.206 5170 Planarity : 0.005 0.100 6011 Dihedral : 9.589 153.996 4895 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.83 % Allowed : 20.13 % Favored : 76.03 % 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: -0.10 (0.13), residues: 4160 helix: 0.98 (0.12), residues: 1881 sheet: -1.14 (0.27), residues: 358 loop : -0.87 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 159 TYR 0.022 0.002 TYR s 43 PHE 0.021 0.002 PHE H 130 TRP 0.022 0.001 TRP Z 142 HIS 0.007 0.001 HIS P 216 Details of bonding type rmsd covalent geometry : bond 0.00363 (34908) covalent geometry : angle 0.63434 (47309) SS BOND : bond 0.00837 ( 3) SS BOND : angle 1.93565 ( 6) hydrogen bonds : bond 0.04200 ( 1439) hydrogen bonds : angle 4.84195 ( 4158) metal coordination : bond 0.01772 ( 37) metal coordination : angle 12.29461 ( 84) Misc. bond : bond 0.00133 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 817 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.9040 (mm) cc_final: 0.8673 (mm) REVERT: A 16 THR cc_start: 0.9075 (m) cc_final: 0.8747 (p) REVERT: B 122 ARG cc_start: 0.8255 (mmm160) cc_final: 0.8051 (mmm160) REVERT: B 127 GLN cc_start: 0.8831 (mt0) cc_final: 0.8512 (mt0) REVERT: D 185 MET cc_start: 0.8547 (tpp) cc_final: 0.7936 (tpp) REVERT: D 443 MET cc_start: 0.8584 (mpp) cc_final: 0.8247 (mpp) REVERT: E 46 ASN cc_start: 0.7297 (t0) cc_final: 0.6707 (t0) REVERT: E 53 ASP cc_start: 0.7989 (p0) cc_final: 0.7718 (t0) REVERT: E 129 TYR cc_start: 0.8488 (m-80) cc_final: 0.8276 (m-10) REVERT: E 194 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: F 217 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7640 (tt0) REVERT: F 246 GLU cc_start: 0.8571 (tt0) cc_final: 0.8354 (tt0) REVERT: F 420 GLU cc_start: 0.7818 (tp30) cc_final: 0.7351 (tp30) REVERT: G 77 MET cc_start: 0.8960 (tpt) cc_final: 0.8482 (tpt) REVERT: G 114 GLU cc_start: 0.8262 (tt0) cc_final: 0.7770 (tm-30) REVERT: G 202 ASN cc_start: 0.7867 (m110) cc_final: 0.7489 (m110) REVERT: G 205 GLN cc_start: 0.8709 (mt0) cc_final: 0.8419 (mp10) REVERT: G 315 THR cc_start: 0.9073 (m) cc_final: 0.8867 (p) REVERT: G 370 GLU cc_start: 0.8309 (tp30) cc_final: 0.7952 (mm-30) REVERT: G 558 GLN cc_start: 0.8006 (tt0) cc_final: 0.7624 (mm-40) REVERT: G 581 ASP cc_start: 0.8902 (m-30) cc_final: 0.8590 (m-30) REVERT: G 628 GLU cc_start: 0.8704 (tp30) cc_final: 0.8337 (tp30) REVERT: H 47 GLN cc_start: 0.8880 (tp40) cc_final: 0.8625 (tp40) REVERT: H 53 MET cc_start: 0.8786 (mtt) cc_final: 0.8577 (mtp) REVERT: H 183 MET cc_start: 0.8623 (mtt) cc_final: 0.8396 (mtp) REVERT: H 214 GLU cc_start: 0.7450 (mp0) cc_final: 0.7201 (mp0) REVERT: H 248 TYR cc_start: 0.7875 (m-80) cc_final: 0.7631 (m-80) REVERT: H 287 HIS cc_start: 0.8389 (m-70) cc_final: 0.8146 (m-70) REVERT: H 291 LYS cc_start: 0.9102 (tppt) cc_final: 0.7736 (tppt) REVERT: I 76 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.7663 (t80) REVERT: I 208 ASP cc_start: 0.7953 (t0) cc_final: 0.7611 (t0) REVERT: P 140 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7223 (t0) REVERT: P 271 TYR cc_start: 0.8145 (m-80) cc_final: 0.7885 (m-80) REVERT: P 324 ILE cc_start: 0.8611 (mm) cc_final: 0.8365 (mp) REVERT: Q 88 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7731 (mt0) REVERT: R 66 GLN cc_start: 0.6991 (pt0) cc_final: 0.6350 (pt0) REVERT: R 67 GLN cc_start: 0.8454 (tp40) cc_final: 0.8133 (tp40) REVERT: S 43 GLU cc_start: 0.8302 (mp0) cc_final: 0.8009 (mp0) REVERT: S 64 LYS cc_start: 0.7072 (mtmm) cc_final: 0.6739 (pttp) REVERT: T 97 LYS cc_start: 0.7759 (tptp) cc_final: 0.7310 (mmmm) REVERT: T 114 ASP cc_start: 0.8285 (t0) cc_final: 0.7727 (t0) REVERT: T 117 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7502 (mt-10) REVERT: T 139 MET cc_start: 0.7692 (tpp) cc_final: 0.6962 (tpp) REVERT: V 11 LEU cc_start: 0.8199 (mt) cc_final: 0.7893 (mt) REVERT: V 64 ASP cc_start: 0.7631 (t0) cc_final: 0.7414 (t70) REVERT: W 27 ASP cc_start: 0.7953 (p0) cc_final: 0.7707 (p0) REVERT: W 30 GLU cc_start: 0.8609 (tt0) cc_final: 0.8157 (mt-10) REVERT: W 43 TYR cc_start: 0.9017 (t80) cc_final: 0.8658 (t80) REVERT: W 53 MET cc_start: 0.8734 (mtt) cc_final: 0.8509 (mtt) REVERT: W 92 GLU cc_start: 0.8942 (tp30) cc_final: 0.8655 (tp30) REVERT: X 37 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7863 (p0) REVERT: X 90 ASP cc_start: 0.8208 (t0) cc_final: 0.7986 (t0) REVERT: Z 21 TYR cc_start: 0.8381 (p90) cc_final: 0.8076 (p90) REVERT: Z 133 MET cc_start: 0.8492 (tmm) cc_final: 0.7763 (tpp) REVERT: a 28 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8634 (ttmm) REVERT: a 34 LYS cc_start: 0.7939 (ptpt) cc_final: 0.7551 (ptpt) REVERT: a 61 TYR cc_start: 0.7446 (m-80) cc_final: 0.6639 (m-80) REVERT: b 47 LYS cc_start: 0.8443 (tmmt) cc_final: 0.8231 (ttpt) REVERT: b 59 ASP cc_start: 0.7663 (t0) cc_final: 0.7441 (m-30) REVERT: b 71 GLN cc_start: 0.8207 (tt0) cc_final: 0.7899 (mt0) REVERT: q 86 TRP cc_start: 0.8175 (m100) cc_final: 0.7471 (m100) REVERT: q 88 ARG cc_start: 0.7372 (ptt180) cc_final: 0.7166 (ttm170) REVERT: q 143 PRO cc_start: 0.7358 (Cg_endo) cc_final: 0.7077 (Cg_exo) REVERT: r 92 LYS cc_start: 0.7910 (mmpt) cc_final: 0.7451 (mmtm) outliers start: 140 outliers final: 94 residues processed: 898 average time/residue: 0.2060 time to fit residues: 303.9247 Evaluate side-chains 856 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 757 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 88 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 154 LEU Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 88 GLN Chi-restraints excluded: chain Q residue 149 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 124 MET Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 151 optimal weight: 2.9990 chunk 308 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 402 optimal weight: 8.9990 chunk 383 optimal weight: 8.9990 chunk 192 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 377 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 455 GLN G 424 HIS G 482 GLN G 495 ASN G 571 HIS ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN G 663 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 HIS S 25 GLN S 73 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 ASN X 104 GLN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.111951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089543 restraints weight = 73929.562| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.56 r_work: 0.3117 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 34949 Z= 0.242 Angle : 0.888 70.474 47399 Z= 0.360 Chirality : 0.046 0.191 5170 Planarity : 0.005 0.060 6011 Dihedral : 9.531 155.130 4895 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.11 % Allowed : 20.38 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4160 helix: 0.86 (0.12), residues: 1900 sheet: -1.22 (0.26), residues: 365 loop : -0.92 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 159 TYR 0.025 0.002 TYR q 144 PHE 0.027 0.002 PHE S 36 TRP 0.037 0.002 TRP q 89 HIS 0.007 0.002 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00570 (34908) covalent geometry : angle 0.69934 (47309) SS BOND : bond 0.04634 ( 3) SS BOND : angle 3.68440 ( 6) hydrogen bonds : bond 0.04556 ( 1439) hydrogen bonds : angle 4.93473 ( 4158) metal coordination : bond 0.02660 ( 37) metal coordination : angle 12.96460 ( 84) Misc. bond : bond 0.00224 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 778 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.9077 (mm) cc_final: 0.8714 (mm) REVERT: A 27 MET cc_start: 0.7586 (mtp) cc_final: 0.6941 (mtm) REVERT: B 122 ARG cc_start: 0.8376 (mmm160) cc_final: 0.8168 (mmm160) REVERT: B 127 GLN cc_start: 0.8970 (mt0) cc_final: 0.8504 (mt0) REVERT: D 185 MET cc_start: 0.8649 (tpp) cc_final: 0.8004 (tpp) REVERT: D 262 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8940 (mp) REVERT: D 443 MET cc_start: 0.8749 (mpp) cc_final: 0.8411 (mpp) REVERT: E 46 ASN cc_start: 0.7380 (t0) cc_final: 0.6856 (t0) REVERT: E 53 ASP cc_start: 0.7986 (p0) cc_final: 0.7756 (t0) REVERT: E 130 HIS cc_start: 0.8743 (t70) cc_final: 0.8338 (t70) REVERT: E 132 GLN cc_start: 0.8875 (mt0) cc_final: 0.8516 (mt0) REVERT: E 194 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: F 217 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7717 (tt0) REVERT: F 420 GLU cc_start: 0.8059 (tp30) cc_final: 0.7622 (tp30) REVERT: G 77 MET cc_start: 0.8928 (tpt) cc_final: 0.8519 (tpt) REVERT: G 114 GLU cc_start: 0.8464 (tt0) cc_final: 0.8110 (tm-30) REVERT: G 202 ASN cc_start: 0.8010 (m110) cc_final: 0.7669 (m110) REVERT: G 205 GLN cc_start: 0.8819 (mt0) cc_final: 0.8406 (mp10) REVERT: G 315 THR cc_start: 0.9062 (m) cc_final: 0.8857 (p) REVERT: G 370 GLU cc_start: 0.8383 (tp30) cc_final: 0.7963 (mm-30) REVERT: G 558 GLN cc_start: 0.8142 (tt0) cc_final: 0.7688 (mm-40) REVERT: G 571 HIS cc_start: 0.9179 (OUTLIER) cc_final: 0.8397 (p90) REVERT: G 581 ASP cc_start: 0.8911 (m-30) cc_final: 0.8620 (m-30) REVERT: G 628 GLU cc_start: 0.8748 (tp30) cc_final: 0.8435 (tp30) REVERT: H 33 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8300 (mt) REVERT: H 47 GLN cc_start: 0.8980 (tp40) cc_final: 0.8690 (tp40) REVERT: H 53 MET cc_start: 0.8811 (mtt) cc_final: 0.8601 (mtp) REVERT: H 183 MET cc_start: 0.8774 (mtt) cc_final: 0.8521 (mtp) REVERT: H 251 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8027 (pp) REVERT: H 291 LYS cc_start: 0.9215 (tppt) cc_final: 0.7722 (tppt) REVERT: I 76 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.7791 (t80) REVERT: P 140 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7429 (t0) REVERT: P 271 TYR cc_start: 0.8339 (m-80) cc_final: 0.8028 (m-80) REVERT: P 296 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.4787 (m-80) REVERT: P 324 ILE cc_start: 0.8600 (mm) cc_final: 0.8352 (mp) REVERT: R 66 GLN cc_start: 0.7016 (pt0) cc_final: 0.6355 (pt0) REVERT: R 67 GLN cc_start: 0.8512 (tp40) cc_final: 0.8208 (tp40) REVERT: S 43 GLU cc_start: 0.8490 (mp0) cc_final: 0.8191 (mp0) REVERT: S 64 LYS cc_start: 0.7360 (mtmm) cc_final: 0.6983 (pttm) REVERT: T 97 LYS cc_start: 0.7945 (tptp) cc_final: 0.7411 (mmmm) REVERT: T 114 ASP cc_start: 0.8435 (t0) cc_final: 0.8048 (t0) REVERT: T 117 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7573 (mt-10) REVERT: T 142 GLN cc_start: 0.8727 (tp40) cc_final: 0.8326 (mm-40) REVERT: V 64 ASP cc_start: 0.7825 (t0) cc_final: 0.7614 (t70) REVERT: W 43 TYR cc_start: 0.9086 (t80) cc_final: 0.8807 (t80) REVERT: X 37 ASP cc_start: 0.8192 (p0) cc_final: 0.7799 (p0) REVERT: Z 10 MET cc_start: 0.8612 (mmm) cc_final: 0.8407 (mmm) REVERT: Z 21 TYR cc_start: 0.8563 (p90) cc_final: 0.8264 (p90) REVERT: Z 51 MET cc_start: 0.8359 (ttm) cc_final: 0.8159 (ttm) REVERT: Z 133 MET cc_start: 0.8514 (tmm) cc_final: 0.8175 (tpp) REVERT: Z 138 PHE cc_start: 0.8402 (m-80) cc_final: 0.8189 (m-80) REVERT: a 61 TYR cc_start: 0.7510 (m-80) cc_final: 0.6598 (m-80) REVERT: a 66 LEU cc_start: 0.7645 (mt) cc_final: 0.7320 (mt) REVERT: b 32 MET cc_start: 0.8783 (tpt) cc_final: 0.8531 (tpp) REVERT: b 47 LYS cc_start: 0.8510 (tmmt) cc_final: 0.8271 (ttpt) REVERT: b 71 GLN cc_start: 0.8273 (tt0) cc_final: 0.7994 (mt0) REVERT: q 60 ARG cc_start: 0.7375 (mtt180) cc_final: 0.7083 (mtm-85) REVERT: q 86 TRP cc_start: 0.8164 (m100) cc_final: 0.7383 (m100) REVERT: q 143 PRO cc_start: 0.7426 (Cg_endo) cc_final: 0.7161 (Cg_exo) outliers start: 150 outliers final: 104 residues processed: 866 average time/residue: 0.2068 time to fit residues: 294.7890 Evaluate side-chains 834 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 722 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 88 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 164 ASN Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 605 GLN Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 663 ASN Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 159 GLN Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 40 ARG Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain T residue 92 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 104 GLN Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 408 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 385 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 364 optimal weight: 0.0070 chunk 302 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 109 optimal weight: 0.2980 chunk 299 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN F 284 HIS F 455 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS G 571 HIS ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN G 663 ASN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN H 287 HIS ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.091331 restraints weight = 73671.907| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.58 r_work: 0.3147 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34949 Z= 0.157 Angle : 0.851 71.626 47399 Z= 0.336 Chirality : 0.044 0.230 5170 Planarity : 0.005 0.052 6011 Dihedral : 9.297 154.582 4895 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.70 % Allowed : 21.50 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4160 helix: 0.98 (0.12), residues: 1893 sheet: -1.08 (0.27), residues: 347 loop : -0.82 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG r 103 TYR 0.026 0.002 TYR H 142 PHE 0.016 0.001 PHE X 70 TRP 0.029 0.001 TRP Q 166 HIS 0.012 0.001 HIS G 572 Details of bonding type rmsd covalent geometry : bond 0.00366 (34908) covalent geometry : angle 0.66315 (47309) SS BOND : bond 0.00667 ( 3) SS BOND : angle 2.30416 ( 6) hydrogen bonds : bond 0.04183 ( 1439) hydrogen bonds : angle 4.81032 ( 4158) metal coordination : bond 0.01768 ( 37) metal coordination : angle 12.69104 ( 84) Misc. bond : bond 0.00164 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 785 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.9051 (mm) cc_final: 0.8706 (mm) REVERT: A 16 THR cc_start: 0.9081 (m) cc_final: 0.8757 (p) REVERT: A 27 MET cc_start: 0.7649 (mtp) cc_final: 0.7111 (mtm) REVERT: B 122 ARG cc_start: 0.8349 (mmm160) cc_final: 0.8124 (mmm160) REVERT: B 127 GLN cc_start: 0.8867 (mt0) cc_final: 0.8480 (mt0) REVERT: D 107 ARG cc_start: 0.8500 (mmt-90) cc_final: 0.8165 (mpt180) REVERT: D 160 ASN cc_start: 0.9065 (t0) cc_final: 0.8620 (t0) REVERT: D 185 MET cc_start: 0.8580 (tpp) cc_final: 0.8017 (tpp) REVERT: D 356 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8903 (pp) REVERT: D 376 GLU cc_start: 0.8063 (mp0) cc_final: 0.7653 (mp0) REVERT: D 443 MET cc_start: 0.8713 (mpp) cc_final: 0.8307 (mpp) REVERT: E 46 ASN cc_start: 0.7357 (t0) cc_final: 0.6678 (t0) REVERT: E 53 ASP cc_start: 0.7993 (p0) cc_final: 0.7791 (t0) REVERT: E 69 TYR cc_start: 0.8033 (m-80) cc_final: 0.7828 (m-80) REVERT: E 194 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: E 222 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5827 (t80) REVERT: F 217 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7709 (tt0) REVERT: F 420 GLU cc_start: 0.7969 (tp30) cc_final: 0.7599 (tp30) REVERT: G 77 MET cc_start: 0.8903 (tpt) cc_final: 0.8546 (tpt) REVERT: G 114 GLU cc_start: 0.8399 (tt0) cc_final: 0.8059 (tm-30) REVERT: G 205 GLN cc_start: 0.8792 (mt0) cc_final: 0.8390 (mp10) REVERT: G 315 THR cc_start: 0.9055 (m) cc_final: 0.8828 (p) REVERT: G 370 GLU cc_start: 0.8283 (tp30) cc_final: 0.7842 (mm-30) REVERT: G 571 HIS cc_start: 0.9082 (OUTLIER) cc_final: 0.8456 (p90) REVERT: G 581 ASP cc_start: 0.8904 (m-30) cc_final: 0.8607 (m-30) REVERT: G 628 GLU cc_start: 0.8747 (tp30) cc_final: 0.8436 (tp30) REVERT: H 33 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8276 (mt) REVERT: H 47 GLN cc_start: 0.8849 (tp40) cc_final: 0.8613 (tp40) REVERT: H 53 MET cc_start: 0.8800 (mtt) cc_final: 0.8592 (mtp) REVERT: H 251 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8058 (pp) REVERT: H 265 LEU cc_start: 0.8687 (mt) cc_final: 0.8448 (tt) REVERT: H 291 LYS cc_start: 0.9180 (tppt) cc_final: 0.7971 (mmmt) REVERT: I 68 ARG cc_start: 0.8769 (ttm-80) cc_final: 0.8190 (mtt180) REVERT: I 76 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.7904 (t80) REVERT: I 89 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: I 208 ASP cc_start: 0.8113 (t0) cc_final: 0.7793 (t0) REVERT: P 140 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7377 (t0) REVERT: P 271 TYR cc_start: 0.8331 (m-80) cc_final: 0.8098 (m-80) REVERT: P 296 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.4681 (m-80) REVERT: P 324 ILE cc_start: 0.8620 (mm) cc_final: 0.8372 (mp) REVERT: Q 124 MET cc_start: 0.8527 (ttm) cc_final: 0.8272 (ttm) REVERT: R 45 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7664 (mtm110) REVERT: R 66 GLN cc_start: 0.7065 (pt0) cc_final: 0.6366 (pt0) REVERT: R 67 GLN cc_start: 0.8508 (tp40) cc_final: 0.8201 (tp40) REVERT: S 43 GLU cc_start: 0.8495 (mp0) cc_final: 0.8204 (mp0) REVERT: S 64 LYS cc_start: 0.7407 (mtmm) cc_final: 0.7079 (pttm) REVERT: T 97 LYS cc_start: 0.8045 (tptp) cc_final: 0.7439 (mmmm) REVERT: T 114 ASP cc_start: 0.8436 (t0) cc_final: 0.8079 (t0) REVERT: T 117 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7567 (mt-10) REVERT: T 139 MET cc_start: 0.7773 (tpp) cc_final: 0.7211 (tpp) REVERT: W 43 TYR cc_start: 0.9062 (t80) cc_final: 0.8721 (t80) REVERT: W 92 GLU cc_start: 0.8971 (tp30) cc_final: 0.8747 (tp30) REVERT: X 37 ASP cc_start: 0.8111 (p0) cc_final: 0.7856 (p0) REVERT: Z 21 TYR cc_start: 0.8557 (p90) cc_final: 0.8261 (p90) REVERT: Z 133 MET cc_start: 0.8471 (tmm) cc_final: 0.8152 (tpp) REVERT: a 61 TYR cc_start: 0.7568 (m-80) cc_final: 0.6626 (m-80) REVERT: b 47 LYS cc_start: 0.8547 (tmmt) cc_final: 0.8339 (ttpt) REVERT: b 59 ASP cc_start: 0.7809 (t0) cc_final: 0.7502 (m-30) REVERT: b 71 GLN cc_start: 0.8214 (tt0) cc_final: 0.7923 (mt0) REVERT: q 86 TRP cc_start: 0.8133 (m100) cc_final: 0.7303 (m100) REVERT: q 143 PRO cc_start: 0.7570 (Cg_endo) cc_final: 0.7329 (Cg_exo) outliers start: 135 outliers final: 94 residues processed: 864 average time/residue: 0.2022 time to fit residues: 287.3899 Evaluate side-chains 831 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 727 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 88 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 162 ASP Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 605 GLN Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 663 ASN Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 40 ARG Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 92 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 2 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 407 optimal weight: 0.4980 chunk 217 optimal weight: 0.9980 chunk 402 optimal weight: 0.7980 chunk 200 optimal weight: 0.5980 chunk 235 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 297 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 455 GLN G 74 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS G 571 HIS ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN G 663 ASN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 73 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN X 124 GLN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093150 restraints weight = 73076.499| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.57 r_work: 0.3175 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 34949 Z= 0.135 Angle : 0.849 73.678 47399 Z= 0.332 Chirality : 0.043 0.207 5170 Planarity : 0.005 0.073 6011 Dihedral : 9.083 154.171 4895 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.12 % Allowed : 22.76 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.13), residues: 4160 helix: 1.08 (0.12), residues: 1889 sheet: -0.94 (0.27), residues: 354 loop : -0.82 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG r 103 TYR 0.027 0.002 TYR q 144 PHE 0.018 0.001 PHE A 51 TRP 0.046 0.001 TRP q 89 HIS 0.018 0.001 HIS G 572 Details of bonding type rmsd covalent geometry : bond 0.00309 (34908) covalent geometry : angle 0.66071 (47309) SS BOND : bond 0.00561 ( 3) SS BOND : angle 1.87662 ( 6) hydrogen bonds : bond 0.03993 ( 1439) hydrogen bonds : angle 4.76356 ( 4158) metal coordination : bond 0.01378 ( 37) metal coordination : angle 12.66064 ( 84) Misc. bond : bond 0.00132 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 761 time to evaluate : 1.333 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 7 ILE cc_start: 0.9015 (mm) cc_final: 0.8652 (mm) REVERT: A 16 THR cc_start: 0.9037 (m) cc_final: 0.8745 (p) REVERT: A 27 MET cc_start: 0.7645 (mtp) cc_final: 0.7154 (mtm) REVERT: B 122 ARG cc_start: 0.8316 (mmm160) cc_final: 0.8073 (mmm160) REVERT: B 127 GLN cc_start: 0.8802 (mt0) cc_final: 0.8424 (mt0) REVERT: D 107 ARG cc_start: 0.8493 (mmt-90) cc_final: 0.8137 (mpt180) REVERT: D 160 ASN cc_start: 0.9066 (t0) cc_final: 0.8627 (t0) REVERT: D 185 MET cc_start: 0.8567 (tpp) cc_final: 0.8164 (tpp) REVERT: D 356 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8900 (pp) REVERT: D 443 MET cc_start: 0.8663 (mpp) cc_final: 0.8348 (mpp) REVERT: E 46 ASN cc_start: 0.7328 (t0) cc_final: 0.6789 (t0) REVERT: E 130 HIS cc_start: 0.8572 (t70) cc_final: 0.7948 (t70) REVERT: E 132 GLN cc_start: 0.8911 (mt0) cc_final: 0.8303 (mp10) REVERT: E 153 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7904 (ttm110) REVERT: E 194 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: F 217 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7469 (tt0) REVERT: F 420 GLU cc_start: 0.7869 (tp30) cc_final: 0.7455 (tp30) REVERT: G 77 MET cc_start: 0.8868 (tpt) cc_final: 0.8550 (tpt) REVERT: G 114 GLU cc_start: 0.8368 (tt0) cc_final: 0.8032 (tm-30) REVERT: G 205 GLN cc_start: 0.8771 (mt0) cc_final: 0.8376 (mp10) REVERT: G 315 THR cc_start: 0.9047 (m) cc_final: 0.8845 (p) REVERT: G 370 GLU cc_start: 0.8260 (tp30) cc_final: 0.7771 (mm-30) REVERT: G 571 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.8605 (p90) REVERT: G 581 ASP cc_start: 0.8906 (m-30) cc_final: 0.8581 (m-30) REVERT: G 605 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: G 628 GLU cc_start: 0.8759 (tp30) cc_final: 0.8374 (tp30) REVERT: H 33 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8328 (mt) REVERT: H 53 MET cc_start: 0.8764 (mtt) cc_final: 0.8518 (mtp) REVERT: H 251 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8014 (pp) REVERT: H 265 LEU cc_start: 0.8724 (mt) cc_final: 0.8458 (tt) REVERT: H 282 TYR cc_start: 0.8926 (t80) cc_final: 0.8622 (t80) REVERT: H 291 LYS cc_start: 0.9131 (tppt) cc_final: 0.8143 (mmmt) REVERT: I 76 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7895 (t80) REVERT: I 89 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: I 188 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8398 (mm-30) REVERT: I 208 ASP cc_start: 0.8100 (t0) cc_final: 0.7792 (t0) REVERT: P 140 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7334 (t0) REVERT: P 271 TYR cc_start: 0.8338 (m-80) cc_final: 0.8134 (m-80) REVERT: P 324 ILE cc_start: 0.8623 (mm) cc_final: 0.8380 (mp) REVERT: Q 60 ASP cc_start: 0.8215 (t0) cc_final: 0.8000 (t0) REVERT: Q 124 MET cc_start: 0.8523 (ttm) cc_final: 0.8269 (ttm) REVERT: Q 157 SER cc_start: 0.8723 (p) cc_final: 0.8417 (m) REVERT: R 66 GLN cc_start: 0.7080 (pt0) cc_final: 0.6382 (pt0) REVERT: R 67 GLN cc_start: 0.8545 (tp40) cc_final: 0.8221 (tp40) REVERT: S 43 GLU cc_start: 0.8499 (mp0) cc_final: 0.8208 (mp0) REVERT: S 62 GLN cc_start: 0.8314 (pt0) cc_final: 0.7792 (pt0) REVERT: S 64 LYS cc_start: 0.7479 (mtmm) cc_final: 0.7109 (pttm) REVERT: S 71 PHE cc_start: 0.8608 (m-10) cc_final: 0.8134 (m-80) REVERT: T 97 LYS cc_start: 0.7888 (tptp) cc_final: 0.7413 (mmmm) REVERT: T 114 ASP cc_start: 0.8438 (t0) cc_final: 0.8058 (t0) REVERT: T 117 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7508 (mt-10) REVERT: T 142 GLN cc_start: 0.8691 (tp40) cc_final: 0.8285 (mm-40) REVERT: W 43 TYR cc_start: 0.9023 (t80) cc_final: 0.8615 (t80) REVERT: W 53 MET cc_start: 0.8595 (mtt) cc_final: 0.8234 (mtt) REVERT: X 37 ASP cc_start: 0.8074 (p0) cc_final: 0.7418 (t0) REVERT: Z 21 TYR cc_start: 0.8568 (p90) cc_final: 0.8271 (p90) REVERT: Z 66 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6988 (mt-10) REVERT: Z 133 MET cc_start: 0.8440 (tmm) cc_final: 0.8132 (tpp) REVERT: a 61 TYR cc_start: 0.7717 (m-80) cc_final: 0.6754 (m-80) REVERT: b 32 MET cc_start: 0.8718 (tpt) cc_final: 0.8386 (tpp) REVERT: b 47 LYS cc_start: 0.8506 (tmmt) cc_final: 0.8303 (ttpt) REVERT: b 59 ASP cc_start: 0.7783 (t0) cc_final: 0.7486 (m-30) REVERT: b 71 GLN cc_start: 0.8194 (tt0) cc_final: 0.7912 (mt0) REVERT: q 86 TRP cc_start: 0.8049 (m100) cc_final: 0.7342 (m100) REVERT: q 143 PRO cc_start: 0.7480 (Cg_endo) cc_final: 0.7236 (Cg_exo) outliers start: 114 outliers final: 83 residues processed: 832 average time/residue: 0.2021 time to fit residues: 276.5937 Evaluate side-chains 804 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 711 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 571 HIS Chi-restraints excluded: chain G residue 605 GLN Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 40 ARG Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 92 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 104 GLN Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 125 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 330 optimal weight: 5.9990 chunk 235 optimal weight: 0.0270 chunk 251 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 314 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 312 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 455 GLN G 123 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS G 571 HIS ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 HIS R 33 HIS S 73 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 95 GLN ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.093461 restraints weight = 73313.225| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.55 r_work: 0.3188 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.6419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34949 Z= 0.140 Angle : 0.858 75.722 47399 Z= 0.335 Chirality : 0.043 0.286 5170 Planarity : 0.005 0.067 6011 Dihedral : 8.946 154.140 4895 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.40 % Allowed : 22.16 % 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: 0.06 (0.13), residues: 4160 helix: 1.08 (0.12), residues: 1886 sheet: -0.89 (0.28), residues: 351 loop : -0.79 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 159 TYR 0.035 0.002 TYR H 142 PHE 0.018 0.001 PHE Q 164 TRP 0.039 0.001 TRP q 89 HIS 0.021 0.001 HIS G 572 Details of bonding type rmsd covalent geometry : bond 0.00327 (34908) covalent geometry : angle 0.66704 (47309) SS BOND : bond 0.00570 ( 3) SS BOND : angle 1.72345 ( 6) hydrogen bonds : bond 0.03924 ( 1439) hydrogen bonds : angle 4.75611 ( 4158) metal coordination : bond 0.01428 ( 37) metal coordination : angle 12.82869 ( 84) Misc. bond : bond 0.00140 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 748 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.9046 (mm) cc_final: 0.8671 (mm) REVERT: A 16 THR cc_start: 0.9050 (m) cc_final: 0.8780 (p) REVERT: A 27 MET cc_start: 0.7698 (mtp) cc_final: 0.7253 (mtm) REVERT: B 127 GLN cc_start: 0.8769 (mt0) cc_final: 0.8435 (mt0) REVERT: D 107 ARG cc_start: 0.8485 (mmt-90) cc_final: 0.8230 (mpt180) REVERT: D 160 ASN cc_start: 0.9065 (t0) cc_final: 0.8642 (t0) REVERT: D 210 MET cc_start: 0.8805 (mtt) cc_final: 0.8463 (mtt) REVERT: D 356 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8915 (pp) REVERT: D 376 GLU cc_start: 0.8086 (mp0) cc_final: 0.7734 (mp0) REVERT: D 443 MET cc_start: 0.8757 (mpp) cc_final: 0.8396 (mpp) REVERT: E 46 ASN cc_start: 0.7338 (t0) cc_final: 0.6656 (t0) REVERT: E 132 GLN cc_start: 0.8866 (mt0) cc_final: 0.8342 (mt0) REVERT: E 194 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: F 217 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7488 (tt0) REVERT: F 420 GLU cc_start: 0.7904 (tp30) cc_final: 0.7486 (tp30) REVERT: G 77 MET cc_start: 0.8851 (tpt) cc_final: 0.8541 (tpt) REVERT: G 114 GLU cc_start: 0.8399 (tt0) cc_final: 0.8071 (tm-30) REVERT: G 205 GLN cc_start: 0.8757 (mt0) cc_final: 0.8488 (mp10) REVERT: G 370 GLU cc_start: 0.8266 (tp30) cc_final: 0.7892 (mm-30) REVERT: G 581 ASP cc_start: 0.8897 (m-30) cc_final: 0.8581 (m-30) REVERT: G 605 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: G 628 GLU cc_start: 0.8773 (tp30) cc_final: 0.8387 (tp30) REVERT: H 33 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8265 (mt) REVERT: H 53 MET cc_start: 0.8782 (mtt) cc_final: 0.8535 (mtp) REVERT: H 54 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8950 (tttp) REVERT: H 251 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8007 (pp) REVERT: H 265 LEU cc_start: 0.8651 (mt) cc_final: 0.8423 (tt) REVERT: H 277 TYR cc_start: 0.8391 (m-10) cc_final: 0.8048 (m-10) REVERT: H 282 TYR cc_start: 0.8896 (t80) cc_final: 0.8548 (t80) REVERT: H 291 LYS cc_start: 0.9119 (tppt) cc_final: 0.8090 (mmmt) REVERT: I 68 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8182 (mtt180) REVERT: I 76 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.7890 (t80) REVERT: I 89 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: I 208 ASP cc_start: 0.8097 (t0) cc_final: 0.7822 (t0) REVERT: P 140 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7387 (t0) REVERT: P 324 ILE cc_start: 0.8635 (mm) cc_final: 0.8407 (mp) REVERT: Q 57 GLU cc_start: 0.8751 (mp0) cc_final: 0.8394 (mp0) REVERT: Q 124 MET cc_start: 0.8543 (ttm) cc_final: 0.8283 (ttm) REVERT: Q 157 SER cc_start: 0.8681 (p) cc_final: 0.8396 (m) REVERT: R 40 GLU cc_start: 0.7237 (pt0) cc_final: 0.6979 (mt-10) REVERT: R 45 ARG cc_start: 0.8030 (ttm170) cc_final: 0.7647 (ttp-170) REVERT: R 66 GLN cc_start: 0.7095 (pt0) cc_final: 0.6400 (pt0) REVERT: R 67 GLN cc_start: 0.8570 (tp40) cc_final: 0.8239 (tp40) REVERT: S 43 GLU cc_start: 0.8461 (mp0) cc_final: 0.8185 (mp0) REVERT: S 62 GLN cc_start: 0.8293 (pt0) cc_final: 0.7791 (pt0) REVERT: S 64 LYS cc_start: 0.7541 (mtmm) cc_final: 0.7155 (pttm) REVERT: S 71 PHE cc_start: 0.8569 (m-10) cc_final: 0.8088 (m-80) REVERT: T 97 LYS cc_start: 0.7937 (tptp) cc_final: 0.7459 (mmmm) REVERT: T 114 ASP cc_start: 0.8452 (t0) cc_final: 0.8098 (t0) REVERT: T 117 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7494 (mt-10) REVERT: T 142 GLN cc_start: 0.8698 (tp40) cc_final: 0.8349 (mm-40) REVERT: W 43 TYR cc_start: 0.9016 (t80) cc_final: 0.8597 (t80) REVERT: X 37 ASP cc_start: 0.8101 (p0) cc_final: 0.7541 (t0) REVERT: Z 21 TYR cc_start: 0.8587 (p90) cc_final: 0.8334 (p90) REVERT: Z 66 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6994 (mt-10) REVERT: Z 133 MET cc_start: 0.8461 (tmm) cc_final: 0.8156 (tpp) REVERT: a 61 TYR cc_start: 0.7675 (m-80) cc_final: 0.6742 (m-80) REVERT: b 32 MET cc_start: 0.8725 (tpt) cc_final: 0.8476 (tpp) REVERT: b 59 ASP cc_start: 0.7780 (t0) cc_final: 0.7491 (m-30) REVERT: b 71 GLN cc_start: 0.8170 (tt0) cc_final: 0.7891 (mt0) REVERT: q 86 TRP cc_start: 0.8074 (m100) cc_final: 0.7362 (m100) REVERT: q 143 PRO cc_start: 0.7456 (Cg_endo) cc_final: 0.7229 (Cg_exo) outliers start: 124 outliers final: 88 residues processed: 829 average time/residue: 0.2066 time to fit residues: 282.6362 Evaluate side-chains 811 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 713 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 605 GLN Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 40 ARG Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 92 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 98 optimal weight: 6.9990 chunk 367 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 282 optimal weight: 0.5980 chunk 346 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 191 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN D 79 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 455 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS P 72 HIS S 73 GLN T 103 HIS ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.115288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093508 restraints weight = 73684.981| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.55 r_work: 0.3189 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34949 Z= 0.141 Angle : 0.870 76.387 47399 Z= 0.341 Chirality : 0.044 0.282 5170 Planarity : 0.005 0.065 6011 Dihedral : 8.888 154.214 4895 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.88 % Allowed : 22.62 % Favored : 74.50 % 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: 0.06 (0.13), residues: 4160 helix: 1.08 (0.12), residues: 1884 sheet: -0.99 (0.27), residues: 363 loop : -0.76 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG r 103 TYR 0.038 0.002 TYR E 129 PHE 0.014 0.001 PHE E 242 TRP 0.035 0.001 TRP q 89 HIS 0.007 0.001 HIS G 571 Details of bonding type rmsd covalent geometry : bond 0.00332 (34908) covalent geometry : angle 0.67904 (47309) SS BOND : bond 0.00620 ( 3) SS BOND : angle 3.38906 ( 6) hydrogen bonds : bond 0.03902 ( 1439) hydrogen bonds : angle 4.77521 ( 4158) metal coordination : bond 0.01464 ( 37) metal coordination : angle 12.92042 ( 84) Misc. bond : bond 0.00144 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8320 Ramachandran restraints generated. 4160 Oldfield, 0 Emsley, 4160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 747 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.9005 (mm) cc_final: 0.8636 (mm) REVERT: B 127 GLN cc_start: 0.8796 (mt0) cc_final: 0.8540 (mt0) REVERT: D 107 ARG cc_start: 0.8427 (mmt-90) cc_final: 0.8141 (mpt180) REVERT: D 210 MET cc_start: 0.8794 (mtt) cc_final: 0.8451 (mtt) REVERT: D 356 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8916 (pp) REVERT: D 376 GLU cc_start: 0.8069 (mp0) cc_final: 0.7714 (mp0) REVERT: D 443 MET cc_start: 0.8788 (mpp) cc_final: 0.8393 (mpp) REVERT: E 46 ASN cc_start: 0.7258 (t0) cc_final: 0.6801 (t0) REVERT: E 71 GLU cc_start: 0.8349 (tp30) cc_final: 0.8031 (mp0) REVERT: E 130 HIS cc_start: 0.8486 (t70) cc_final: 0.7767 (t70) REVERT: E 193 GLU cc_start: 0.8581 (pm20) cc_final: 0.7777 (pt0) REVERT: E 194 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: F 217 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7555 (tt0) REVERT: F 420 GLU cc_start: 0.7958 (tp30) cc_final: 0.7548 (tp30) REVERT: G 77 MET cc_start: 0.8847 (tpt) cc_final: 0.8538 (tpt) REVERT: G 114 GLU cc_start: 0.8445 (tt0) cc_final: 0.8112 (tm-30) REVERT: G 205 GLN cc_start: 0.8766 (mt0) cc_final: 0.8434 (mp10) REVERT: G 370 GLU cc_start: 0.8256 (tp30) cc_final: 0.7884 (mm-30) REVERT: G 581 ASP cc_start: 0.8880 (m-30) cc_final: 0.8563 (m-30) REVERT: G 605 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: G 628 GLU cc_start: 0.8785 (tp30) cc_final: 0.8396 (tp30) REVERT: H 17 MET cc_start: 0.8684 (tmm) cc_final: 0.8432 (tmm) REVERT: H 33 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8338 (mt) REVERT: H 53 MET cc_start: 0.8811 (mtt) cc_final: 0.8594 (mtp) REVERT: H 54 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8904 (tttp) REVERT: H 172 MET cc_start: 0.8419 (ppp) cc_final: 0.7946 (ppp) REVERT: H 251 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7979 (pp) REVERT: H 265 LEU cc_start: 0.8667 (mt) cc_final: 0.8443 (tt) REVERT: H 277 TYR cc_start: 0.8331 (m-10) cc_final: 0.8029 (m-10) REVERT: H 282 TYR cc_start: 0.8893 (t80) cc_final: 0.8571 (t80) REVERT: H 291 LYS cc_start: 0.9082 (tppt) cc_final: 0.8052 (mmmt) REVERT: I 76 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.7892 (t80) REVERT: I 89 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: I 208 ASP cc_start: 0.8074 (t0) cc_final: 0.7805 (t0) REVERT: P 137 ARG cc_start: 0.7380 (ttm110) cc_final: 0.7111 (ttp-110) REVERT: P 140 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7398 (t0) REVERT: P 324 ILE cc_start: 0.8615 (mm) cc_final: 0.8390 (mp) REVERT: Q 57 GLU cc_start: 0.8702 (mp0) cc_final: 0.8429 (mp0) REVERT: Q 87 MET cc_start: 0.8799 (mmm) cc_final: 0.8310 (mmt) REVERT: Q 124 MET cc_start: 0.8556 (ttm) cc_final: 0.8289 (ttm) REVERT: Q 157 SER cc_start: 0.8667 (p) cc_final: 0.8390 (m) REVERT: R 66 GLN cc_start: 0.7108 (pt0) cc_final: 0.6408 (pt0) REVERT: R 67 GLN cc_start: 0.8556 (tp40) cc_final: 0.8120 (tp40) REVERT: S 43 GLU cc_start: 0.8444 (mp0) cc_final: 0.8176 (mp0) REVERT: S 62 GLN cc_start: 0.8298 (pt0) cc_final: 0.7793 (pt0) REVERT: S 64 LYS cc_start: 0.7642 (mtmm) cc_final: 0.7202 (pttm) REVERT: S 71 PHE cc_start: 0.8602 (m-10) cc_final: 0.8112 (m-80) REVERT: T 97 LYS cc_start: 0.7976 (tptp) cc_final: 0.7474 (mmmm) REVERT: T 114 ASP cc_start: 0.8474 (t0) cc_final: 0.8119 (t0) REVERT: T 117 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7490 (mt-10) REVERT: T 139 MET cc_start: 0.7709 (tpp) cc_final: 0.6601 (tpp) REVERT: T 142 GLN cc_start: 0.8689 (tp40) cc_final: 0.8356 (mm-40) REVERT: W 43 TYR cc_start: 0.9009 (t80) cc_final: 0.8568 (t80) REVERT: X 37 ASP cc_start: 0.8012 (p0) cc_final: 0.7486 (t0) REVERT: Z 21 TYR cc_start: 0.8608 (p90) cc_final: 0.8374 (p90) REVERT: Z 66 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7027 (mt-10) REVERT: Z 133 MET cc_start: 0.8466 (tmm) cc_final: 0.8165 (tpp) REVERT: a 53 ARG cc_start: 0.8329 (mtt90) cc_final: 0.7598 (ttt-90) REVERT: a 61 TYR cc_start: 0.7689 (m-80) cc_final: 0.6741 (m-80) REVERT: b 59 ASP cc_start: 0.7766 (t0) cc_final: 0.7428 (m-30) REVERT: b 71 GLN cc_start: 0.8173 (tt0) cc_final: 0.7902 (mt0) REVERT: q 86 TRP cc_start: 0.8047 (m100) cc_final: 0.7350 (m100) outliers start: 105 outliers final: 83 residues processed: 817 average time/residue: 0.2032 time to fit residues: 273.4095 Evaluate side-chains 803 residues out of total 3651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 710 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 605 GLN Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 671 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 149 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 40 ARG Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 92 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 129 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 351 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 302 optimal weight: 0.0980 chunk 213 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 455 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN P 72 HIS ** P 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.113547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.091541 restraints weight = 74045.553| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.55 r_work: 0.3158 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34949 Z= 0.178 Angle : 0.890 77.506 47399 Z= 0.351 Chirality : 0.045 0.327 5170 Planarity : 0.005 0.064 6011 Dihedral : 8.878 154.412 4895 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.99 % Allowed : 22.82 % Favored : 74.20 % 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: 0.02 (0.13), residues: 4160 helix: 1.05 (0.12), residues: 1887 sheet: -1.05 (0.27), residues: 373 loop : -0.77 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 122 TYR 0.031 0.002 TYR q 144 PHE 0.022 0.001 PHE G 214 TRP 0.031 0.002 TRP q 89 HIS 0.006 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00423 (34908) covalent geometry : angle 0.69202 (47309) SS BOND : bond 0.00881 ( 3) SS BOND : angle 3.51203 ( 6) hydrogen bonds : bond 0.04037 ( 1439) hydrogen bonds : angle 4.81695 ( 4158) metal coordination : bond 0.01909 ( 37) metal coordination : angle 13.29529 ( 84) Misc. bond : bond 0.00183 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9249.99 seconds wall clock time: 159 minutes 7.82 seconds (9547.82 seconds total)