Starting phenix.real_space_refine on Sat Feb 17 04:28:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/02_2024/8d3l_27159_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/02_2024/8d3l_27159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/02_2024/8d3l_27159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/02_2024/8d3l_27159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/02_2024/8d3l_27159_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3l_27159/02_2024/8d3l_27159_updated.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.028 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 Mn 2 7.51 5 Fe 8 7.16 5 P 63 5.49 5 S 106 5.16 5 C 10874 2.51 5 N 3066 2.21 5 O 3366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F GLU 91": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J GLU 154": "OE1" <-> "OE2" Residue "J GLU 177": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17485 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2768 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 331} Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2758 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 11, 'TRANS': 330} Chain: "C" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2768 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 331} Chain: "D" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2758 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 11, 'TRANS': 330} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 771 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 771 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "G" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 671 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 653 Classifications: {'DNA': 32} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 31} Chain: "I" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1775 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "J" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1770 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14084 SG CYS I 21 44.947 62.454 123.034 1.00 8.72 S ATOM 15460 SG CYS I 190 44.559 60.728 119.782 1.00 10.07 S ATOM 15460 SG CYS I 190 44.559 60.728 119.782 1.00 10.07 S ATOM 15482 SG CYS I 193 48.647 61.031 119.637 1.00 10.89 S ATOM 15525 SG CYS I 199 47.994 58.265 120.908 1.00 7.81 S ATOM 15525 SG CYS I 199 47.994 58.265 120.908 1.00 7.81 S ATOM 14084 SG CYS I 21 44.947 62.454 123.034 1.00 8.72 S ATOM 15460 SG CYS I 190 44.559 60.728 119.782 1.00 10.07 S ATOM 15482 SG CYS I 193 48.647 61.031 119.637 1.00 10.89 S ATOM 15854 SG CYS J 21 43.498 43.198 61.747 1.00 3.29 S ATOM 17295 SG CYS J 199 42.009 47.355 61.495 1.00 4.28 S ATOM 17252 SG CYS J 193 45.117 45.989 64.802 1.00 3.36 S ATOM 17295 SG CYS J 199 42.009 47.355 61.495 1.00 4.28 S ATOM 15854 SG CYS J 21 43.498 43.198 61.747 1.00 3.29 S ATOM 17230 SG CYS J 190 42.383 43.388 65.022 1.00 5.47 S ATOM 17252 SG CYS J 193 45.117 45.989 64.802 1.00 3.36 S ATOM 17230 SG CYS J 190 42.383 43.388 65.022 1.00 5.47 S Time building chain proxies: 9.35, per 1000 atoms: 0.53 Number of scatterers: 17485 At special positions: 0 Unit cell: (112.381, 116.006, 175.822, 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) Fe 8 26.01 Mn 2 24.99 S 106 16.00 P 63 15.00 O 3366 8.00 N 3066 7.00 C 10874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.10 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 301 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 190 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 199 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 21 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 193 " pdb=" SF4 J 301 " pdb="FE2 SF4 J 301 " - pdb=" SG CYS J 199 " pdb="FE1 SF4 J 301 " - pdb=" SG CYS J 21 " pdb="FE3 SF4 J 301 " - pdb=" SG CYS J 193 " pdb="FE4 SF4 J 301 " - pdb=" SG CYS J 190 " Number of angles added : 24 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 20 sheets defined 44.1% alpha, 12.6% beta 20 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 6.88 Creating SS restraints... Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 89 through 99 removed outlier: 3.546A pdb=" N GLU A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 removed outlier: 3.586A pdb=" N GLY A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 155 removed outlier: 3.992A pdb=" N ASN A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 180 removed outlier: 4.273A pdb=" N ASP A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLN A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 224 Processing helix chain 'A' and resid 242 through 265 removed outlier: 4.851A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.590A pdb=" N GLN A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 Proline residue: A 319 - end of helix removed outlier: 3.949A pdb=" N GLN A 322 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.526A pdb=" N GLU B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 101 through 129 removed outlier: 3.725A pdb=" N ASN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 154 removed outlier: 3.954A pdb=" N GLN B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 179 removed outlier: 3.760A pdb=" N VAL B 176 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLN B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.822A pdb=" N PHE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 219 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 255 removed outlier: 4.601A pdb=" N GLU B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.846A pdb=" N GLN B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 331 Proline residue: B 319 - end of helix removed outlier: 4.318A pdb=" N GLN B 322 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG B 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 62 removed outlier: 3.655A pdb=" N GLU C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 102 through 129 Processing helix chain 'C' and resid 136 through 154 Processing helix chain 'C' and resid 159 through 178 removed outlier: 3.563A pdb=" N GLN C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN C 172 " --> pdb=" O GLN C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 205 through 222 Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 257 through 267 removed outlier: 4.486A pdb=" N ARG C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 316 through 330 removed outlier: 4.486A pdb=" N TYR C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 88 through 97 Processing helix chain 'D' and resid 101 through 129 Processing helix chain 'D' and resid 136 through 154 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.852A pdb=" N ARG D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 180 removed outlier: 4.183A pdb=" N GLN D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 224 removed outlier: 3.587A pdb=" N VAL D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 246 No H-bonds generated for 'chain 'D' and resid 243 through 246' Processing helix chain 'D' and resid 249 through 255 removed outlier: 4.122A pdb=" N GLY D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 265 Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 316 through 330 removed outlier: 4.474A pdb=" N TYR D 320 " --> pdb=" O GLY D 316 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'F' and resid 16 through 29 removed outlier: 3.549A pdb=" N ASN F 29 " --> pdb=" O LYS F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'I' and resid 12 through 20 removed outlier: 3.706A pdb=" N GLN I 16 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 29 removed outlier: 3.775A pdb=" N ALA I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 49 Processing helix chain 'I' and resid 119 through 134 Processing helix chain 'I' and resid 159 through 178 Processing helix chain 'I' and resid 189 through 191 No H-bonds generated for 'chain 'I' and resid 189 through 191' Processing helix chain 'I' and resid 196 through 199 No H-bonds generated for 'chain 'I' and resid 196 through 199' Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'J' and resid 12 through 15 Processing helix chain 'J' and resid 17 through 19 No H-bonds generated for 'chain 'J' and resid 17 through 19' Processing helix chain 'J' and resid 23 through 29 Processing helix chain 'J' and resid 38 through 50 removed outlier: 4.191A pdb=" N GLU J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 133 Processing helix chain 'J' and resid 159 through 177 removed outlier: 3.996A pdb=" N LYS J 164 " --> pdb=" O ALA J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 191 No H-bonds generated for 'chain 'J' and resid 189 through 191' Processing helix chain 'J' and resid 196 through 199 No H-bonds generated for 'chain 'J' and resid 196 through 199' Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.611A pdb=" N TYR J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.881A pdb=" N ALA A 43 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL A 10 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 45 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER A 66 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLY A 46 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 68 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.796A pdb=" N GLY A 34 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 274 through 276 removed outlier: 4.113A pdb=" N LEU A 283 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 303 through 305 Processing sheet with id= E, first strand: chain 'B' and resid 50 through 52 removed outlier: 6.967A pdb=" N THR B 15 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 34 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS B 28 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 66 through 70 removed outlier: 7.866A pdb=" N ASN B 6 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 44 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 8 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLY B 46 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 10 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 303 through 305 Processing sheet with id= H, first strand: chain 'C' and resid 7 through 10 removed outlier: 7.299A pdb=" N ALA C 43 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N VAL C 10 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 45 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER C 66 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLY C 46 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR C 68 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 16 through 20 removed outlier: 6.224A pdb=" N LYS C 28 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 303 through 305 Processing sheet with id= K, first strand: chain 'D' and resid 16 through 20 removed outlier: 3.915A pdb=" N GLY D 34 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 75 through 77 removed outlier: 3.619A pdb=" N ARG D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D 66 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN D 6 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE D 44 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU D 8 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY D 46 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL D 10 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 274 through 276 Processing sheet with id= N, first strand: chain 'D' and resid 303 through 305 Processing sheet with id= O, first strand: chain 'E' and resid 65 through 72 removed outlier: 6.019A pdb=" N LEU E 2 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN E 35 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLU E 40 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG E 33 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 65 through 72 removed outlier: 7.008A pdb=" N LEU F 2 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU F 40 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG F 33 " --> pdb=" O GLU F 40 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 63 through 66 removed outlier: 7.991A pdb=" N LYS I 141 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N GLU I 108 " --> pdb=" O LYS I 141 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR I 143 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LYS I 110 " --> pdb=" O TYR I 143 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE I 145 " --> pdb=" O LYS I 110 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 68 through 72 Processing sheet with id= S, first strand: chain 'J' and resid 63 through 66 removed outlier: 7.523A pdb=" N TYR J 143 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N LYS J 110 " --> pdb=" O TYR J 143 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE J 145 " --> pdb=" O LYS J 110 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 68 through 72 705 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 7.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 7519 1.42 - 1.64: 10230 1.64 - 1.85: 169 1.85 - 2.07: 1 2.07 - 2.29: 24 Bond restraints: 17943 Sorted by residual: bond pdb=" CA TYR E 7 " pdb=" C TYR E 7 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.21e-02 6.83e+03 1.98e+01 bond pdb=" CA TYR F 7 " pdb=" C TYR F 7 " ideal model delta sigma weight residual 1.523 1.488 0.034 1.25e-02 6.40e+03 7.61e+00 bond pdb=" CA ALA C 204 " pdb=" CB ALA C 204 " ideal model delta sigma weight residual 1.532 1.491 0.040 1.57e-02 4.06e+03 6.62e+00 bond pdb=" CA ASN C 203 " pdb=" C ASN C 203 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.31e-02 5.83e+03 6.48e+00 bond pdb=" C TYR E 7 " pdb=" O TYR E 7 " ideal model delta sigma weight residual 1.234 1.204 0.030 1.28e-02 6.10e+03 5.64e+00 ... (remaining 17938 not shown) Histogram of bond angle deviations from ideal: 73.56 - 85.66: 24 85.66 - 97.77: 0 97.77 - 109.88: 2652 109.88 - 121.99: 18106 121.99 - 134.09: 3683 Bond angle restraints: 24465 Sorted by residual: angle pdb=" N ASN C 203 " pdb=" CA ASN C 203 " pdb=" C ASN C 203 " ideal model delta sigma weight residual 113.89 97.85 16.04 1.58e+00 4.01e-01 1.03e+02 angle pdb=" N PRO C 197 " pdb=" CA PRO C 197 " pdb=" C PRO C 197 " ideal model delta sigma weight residual 110.70 99.98 10.72 1.22e+00 6.72e-01 7.72e+01 angle pdb=" C ARG C 196 " pdb=" N PRO C 197 " pdb=" CA PRO C 197 " ideal model delta sigma weight residual 120.38 115.00 5.38 1.03e+00 9.43e-01 2.73e+01 angle pdb=" N ALA C 204 " pdb=" CA ALA C 204 " pdb=" C ALA C 204 " ideal model delta sigma weight residual 113.12 106.98 6.14 1.25e+00 6.40e-01 2.41e+01 angle pdb=" CA GLU E 62 " pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 ... (remaining 24460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 10068 30.55 - 61.11: 634 61.11 - 91.66: 31 91.66 - 122.22: 0 122.22 - 152.77: 4 Dihedral angle restraints: 10737 sinusoidal: 4910 harmonic: 5827 Sorted by residual: dihedral pdb=" C ARG C 196 " pdb=" N ARG C 196 " pdb=" CA ARG C 196 " pdb=" CB ARG C 196 " ideal model delta harmonic sigma weight residual -122.60 -135.44 12.84 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N ARG C 196 " pdb=" C ARG C 196 " pdb=" CA ARG C 196 " pdb=" CB ARG C 196 " ideal model delta harmonic sigma weight residual 122.80 135.24 -12.44 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA ARG A 196 " pdb=" C ARG A 196 " pdb=" N PRO A 197 " pdb=" CA PRO A 197 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 10734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2632 0.108 - 0.216: 52 0.216 - 0.323: 2 0.323 - 0.431: 0 0.431 - 0.539: 1 Chirality restraints: 2687 Sorted by residual: chirality pdb=" CA ARG C 196 " pdb=" N ARG C 196 " pdb=" C ARG C 196 " pdb=" CB ARG C 196 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" CA ASP C 200 " pdb=" N ASP C 200 " pdb=" C ASP C 200 " pdb=" CB ASP C 200 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ARG C 195 " pdb=" N ARG C 195 " pdb=" C ARG C 195 " pdb=" CB ARG C 195 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2684 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 196 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO A 197 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 92 " -0.041 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO F 93 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 93 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 93 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 306 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO C 307 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.029 5.00e-02 4.00e+02 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 35 2.38 - 3.01: 9347 3.01 - 3.64: 25276 3.64 - 4.27: 36694 4.27 - 4.90: 62026 Nonbonded interactions: 133378 Sorted by model distance: nonbonded pdb=" OP1 DG H 29 " pdb="MN MN I 302 " model vdw 1.752 2.320 nonbonded pdb=" OD2 ASP I 82 " pdb="MN MN I 302 " model vdw 2.032 2.320 nonbonded pdb=" OG SER C 84 " pdb=" OH TYR D 229 " model vdw 2.137 2.440 nonbonded pdb=" OP1 DG G 29 " pdb="MN MN J 302 " model vdw 2.141 2.320 nonbonded pdb=" OG SER I 218 " pdb=" OE1 GLU I 219 " model vdw 2.191 2.440 ... (remaining 133373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 342) selection = chain 'B' selection = (chain 'C' and resid 1 through 342) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 3 through 219 or resid 301 through 302)) selection = chain 'J' } 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.230 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 53.420 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.003 0.087 17943 Z= 0.187 Angle : 0.617 16.036 24465 Z= 0.348 Chirality : 0.041 0.539 2687 Planarity : 0.005 0.116 2912 Dihedral : 17.744 152.772 6983 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.99 % Favored : 93.75 % Rotamer: Outliers : 0.23 % Allowed : 0.74 % Favored : 99.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1985 helix: 1.15 (0.18), residues: 911 sheet: -0.20 (0.32), residues: 258 loop : -1.97 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 296 HIS 0.010 0.001 HIS D 130 PHE 0.026 0.001 PHE D 232 TYR 0.027 0.001 TYR E 7 ARG 0.006 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 260 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 MET cc_start: 0.5562 (mpp) cc_final: 0.4210 (mmt) REVERT: D 178 ASP cc_start: 0.7391 (t0) cc_final: 0.7070 (t0) REVERT: D 197 PRO cc_start: 0.3979 (Cg_exo) cc_final: 0.3654 (Cg_endo) REVERT: D 200 ASP cc_start: 0.6884 (m-30) cc_final: 0.6484 (p0) outliers start: 4 outliers final: 0 residues processed: 262 average time/residue: 0.3035 time to fit residues: 117.5819 Evaluate side-chains 200 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 0.0270 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN B 201 ASN B 322 GLN C 30 GLN C 39 HIS ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 HIS C 322 GLN D 118 ASN D 135 ASN ** D 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN J 32 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 17943 Z= 0.436 Angle : 0.727 9.898 24465 Z= 0.385 Chirality : 0.046 0.172 2687 Planarity : 0.006 0.115 2912 Dihedral : 17.457 157.001 2901 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.36 % Favored : 91.39 % Rotamer: Outliers : 1.37 % Allowed : 11.20 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1985 helix: 1.07 (0.18), residues: 898 sheet: -0.24 (0.33), residues: 240 loop : -2.28 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 342 HIS 0.007 0.002 HIS J 180 PHE 0.028 0.002 PHE C 340 TYR 0.022 0.002 TYR D 255 ARG 0.007 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 MET cc_start: 0.5881 (mpp) cc_final: 0.4327 (mmt) REVERT: D 125 ARG cc_start: 0.6973 (tpp-160) cc_final: 0.6719 (tmt170) REVERT: D 200 ASP cc_start: 0.6923 (m-30) cc_final: 0.6271 (p0) REVERT: D 342 TRP cc_start: 0.8445 (OUTLIER) cc_final: 0.7891 (m-10) REVERT: E 62 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: I 7 ASP cc_start: 0.7274 (t0) cc_final: 0.6929 (t0) REVERT: J 35 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7537 (mm-30) outliers start: 24 outliers final: 19 residues processed: 218 average time/residue: 0.2990 time to fit residues: 98.0444 Evaluate side-chains 212 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain I residue 130 CYS Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 198 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 182 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN D 215 ASN J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17943 Z= 0.176 Angle : 0.548 8.861 24465 Z= 0.294 Chirality : 0.038 0.144 2687 Planarity : 0.005 0.114 2912 Dihedral : 17.222 158.945 2901 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.10 % Favored : 93.80 % Rotamer: Outliers : 1.60 % Allowed : 14.17 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1985 helix: 1.33 (0.18), residues: 900 sheet: 0.00 (0.33), residues: 245 loop : -2.07 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 342 HIS 0.005 0.001 HIS C 39 PHE 0.011 0.001 PHE C 340 TYR 0.011 0.001 TYR D 275 ARG 0.005 0.000 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 2.021 Fit side-chains REVERT: B 125 ARG cc_start: 0.7322 (tmm-80) cc_final: 0.6863 (ttt90) REVERT: B 180 MET cc_start: 0.5761 (mpp) cc_final: 0.4150 (mmt) REVERT: D 125 ARG cc_start: 0.6940 (tpp-160) cc_final: 0.6657 (tmt170) REVERT: D 200 ASP cc_start: 0.6956 (m-30) cc_final: 0.6510 (p0) REVERT: E 62 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: J 35 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7427 (mm-30) outliers start: 28 outliers final: 21 residues processed: 214 average time/residue: 0.3212 time to fit residues: 102.3463 Evaluate side-chains 209 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 191 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS C 87 ASN E 35 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17943 Z= 0.197 Angle : 0.557 13.872 24465 Z= 0.293 Chirality : 0.038 0.145 2687 Planarity : 0.005 0.113 2912 Dihedral : 17.188 158.952 2901 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 2.63 % Allowed : 16.06 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 1985 helix: 1.41 (0.18), residues: 893 sheet: 0.01 (0.33), residues: 246 loop : -1.98 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 342 HIS 0.003 0.001 HIS C 39 PHE 0.026 0.001 PHE D 111 TYR 0.012 0.001 TYR D 337 ARG 0.006 0.000 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 193 time to evaluate : 1.977 Fit side-chains REVERT: B 30 GLN cc_start: 0.6215 (mm-40) cc_final: 0.6007 (mm110) REVERT: B 125 ARG cc_start: 0.7373 (tmm-80) cc_final: 0.6894 (ttt90) REVERT: B 180 MET cc_start: 0.5798 (mpp) cc_final: 0.4732 (mmt) REVERT: D 41 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8270 (mp) REVERT: D 125 ARG cc_start: 0.6976 (tpp-160) cc_final: 0.6680 (tmt170) REVERT: D 178 ASP cc_start: 0.6604 (t0) cc_final: 0.6398 (m-30) REVERT: D 200 ASP cc_start: 0.7158 (m-30) cc_final: 0.6613 (p0) REVERT: D 243 LEU cc_start: 0.2289 (OUTLIER) cc_final: 0.1350 (tp) REVERT: D 342 TRP cc_start: 0.8341 (OUTLIER) cc_final: 0.7617 (m-10) REVERT: E 62 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: I 68 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6220 (tpt) REVERT: J 35 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7381 (mm-30) outliers start: 46 outliers final: 24 residues processed: 228 average time/residue: 0.2919 time to fit residues: 100.9926 Evaluate side-chains 212 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 191 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 2 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 30 GLN C 39 HIS D 183 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN I 44 GLN I 147 ASN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17943 Z= 0.308 Angle : 0.623 9.278 24465 Z= 0.330 Chirality : 0.042 0.196 2687 Planarity : 0.005 0.113 2912 Dihedral : 17.371 159.980 2901 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.61 % Favored : 91.28 % Rotamer: Outliers : 2.91 % Allowed : 17.37 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 1985 helix: 1.18 (0.18), residues: 897 sheet: -0.18 (0.33), residues: 249 loop : -2.13 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 342 HIS 0.005 0.001 HIS J 180 PHE 0.022 0.002 PHE C 340 TYR 0.019 0.001 TYR C 320 ARG 0.004 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 1.889 Fit side-chains REVERT: B 125 ARG cc_start: 0.7438 (tmm-80) cc_final: 0.7024 (ttt90) REVERT: B 180 MET cc_start: 0.5876 (mpp) cc_final: 0.4194 (mmt) REVERT: D 41 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8253 (mp) REVERT: D 200 ASP cc_start: 0.7096 (m-30) cc_final: 0.6629 (p0) REVERT: D 342 TRP cc_start: 0.8427 (OUTLIER) cc_final: 0.7789 (m-10) REVERT: E 62 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: I 68 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6155 (tpt) REVERT: J 35 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7457 (mm-30) outliers start: 51 outliers final: 33 residues processed: 223 average time/residue: 0.2777 time to fit residues: 96.0764 Evaluate side-chains 218 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 191 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 73 ASN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17943 Z= 0.262 Angle : 0.592 11.504 24465 Z= 0.313 Chirality : 0.040 0.145 2687 Planarity : 0.005 0.112 2912 Dihedral : 17.339 161.525 2901 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.96 % Favored : 91.99 % Rotamer: Outliers : 2.97 % Allowed : 18.46 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 1985 helix: 1.21 (0.18), residues: 896 sheet: -0.19 (0.33), residues: 251 loop : -2.12 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 342 HIS 0.004 0.001 HIS D 130 PHE 0.016 0.001 PHE C 340 TYR 0.016 0.001 TYR D 255 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 179 time to evaluate : 2.118 Fit side-chains REVERT: B 125 ARG cc_start: 0.7475 (tmm-80) cc_final: 0.6991 (ttt90) REVERT: B 180 MET cc_start: 0.5910 (mpp) cc_final: 0.4217 (mmt) REVERT: D 41 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8290 (mp) REVERT: D 150 MET cc_start: 0.6700 (ttm) cc_final: 0.6457 (mtp) REVERT: D 183 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: D 200 ASP cc_start: 0.7083 (m-30) cc_final: 0.6780 (p0) REVERT: D 342 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7709 (m-10) REVERT: E 62 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: I 68 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6111 (tpt) REVERT: J 35 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7502 (mm-30) REVERT: J 68 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5387 (ttt) outliers start: 52 outliers final: 33 residues processed: 216 average time/residue: 0.2853 time to fit residues: 94.8757 Evaluate side-chains 216 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 68 MET Chi-restraints excluded: chain J residue 191 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 0.0170 chunk 164 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 194 optimal weight: 0.3980 chunk 121 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 30 GLN C 39 HIS ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17943 Z= 0.161 Angle : 0.534 9.854 24465 Z= 0.284 Chirality : 0.037 0.141 2687 Planarity : 0.004 0.112 2912 Dihedral : 17.139 162.041 2901 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.40 % Favored : 93.55 % Rotamer: Outliers : 2.34 % Allowed : 19.20 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 1985 helix: 1.46 (0.18), residues: 894 sheet: -0.21 (0.32), residues: 269 loop : -2.03 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 165 HIS 0.004 0.001 HIS D 130 PHE 0.012 0.001 PHE D 232 TYR 0.013 0.001 TYR D 255 ARG 0.002 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 2.054 Fit side-chains revert: symmetry clash REVERT: A 224 VAL cc_start: 0.8547 (m) cc_final: 0.8246 (p) REVERT: B 150 MET cc_start: 0.5770 (tpp) cc_final: 0.5182 (tpp) REVERT: D 180 MET cc_start: 0.6000 (tpt) cc_final: 0.5226 (tpt) REVERT: D 200 ASP cc_start: 0.7133 (m-30) cc_final: 0.6799 (p0) REVERT: D 305 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8312 (p) REVERT: D 342 TRP cc_start: 0.8311 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: E 62 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: I 68 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6127 (tpt) REVERT: J 68 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5263 (ttt) outliers start: 41 outliers final: 27 residues processed: 221 average time/residue: 0.2829 time to fit residues: 96.3537 Evaluate side-chains 218 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 68 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN D 215 ASN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17943 Z= 0.341 Angle : 0.649 10.118 24465 Z= 0.343 Chirality : 0.043 0.231 2687 Planarity : 0.005 0.111 2912 Dihedral : 17.483 163.713 2901 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.61 % Favored : 91.18 % Rotamer: Outliers : 3.14 % Allowed : 19.20 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1985 helix: 1.17 (0.18), residues: 891 sheet: -0.32 (0.33), residues: 259 loop : -2.19 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 342 HIS 0.006 0.001 HIS D 39 PHE 0.027 0.002 PHE C 340 TYR 0.022 0.002 TYR C 320 ARG 0.004 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 188 time to evaluate : 1.888 Fit side-chains revert: symmetry clash REVERT: B 125 ARG cc_start: 0.7302 (tmm-80) cc_final: 0.7098 (ttt90) REVERT: B 180 MET cc_start: 0.6014 (mpp) cc_final: 0.4421 (mmt) REVERT: D 200 ASP cc_start: 0.6961 (m-30) cc_final: 0.6743 (p0) REVERT: D 305 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8416 (p) REVERT: D 342 TRP cc_start: 0.8484 (OUTLIER) cc_final: 0.7885 (m-10) REVERT: E 62 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: I 68 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6074 (tpt) REVERT: J 68 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5444 (ttt) outliers start: 55 outliers final: 37 residues processed: 227 average time/residue: 0.2970 time to fit residues: 102.5317 Evaluate side-chains 223 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 68 MET Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 191 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 109 optimal weight: 0.0030 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN E 35 GLN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17943 Z= 0.225 Angle : 0.585 8.920 24465 Z= 0.310 Chirality : 0.039 0.147 2687 Planarity : 0.005 0.111 2912 Dihedral : 17.351 165.010 2901 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 2.46 % Allowed : 19.77 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 1985 helix: 1.25 (0.18), residues: 890 sheet: -0.30 (0.33), residues: 260 loop : -2.11 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 165 HIS 0.005 0.001 HIS D 130 PHE 0.015 0.001 PHE C 340 TYR 0.013 0.001 TYR C 320 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 1.927 Fit side-chains REVERT: B 125 ARG cc_start: 0.7386 (tmm-80) cc_final: 0.6784 (ttt90) REVERT: B 180 MET cc_start: 0.5784 (mpp) cc_final: 0.4224 (mmt) REVERT: D 126 MET cc_start: 0.7375 (tpp) cc_final: 0.6816 (tpp) REVERT: D 200 ASP cc_start: 0.6939 (m-30) cc_final: 0.6674 (p0) REVERT: D 305 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8412 (p) REVERT: D 342 TRP cc_start: 0.8400 (OUTLIER) cc_final: 0.7734 (m-10) REVERT: E 62 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: I 68 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6067 (tpt) REVERT: J 68 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5328 (ttt) outliers start: 43 outliers final: 34 residues processed: 213 average time/residue: 0.3068 time to fit residues: 100.3276 Evaluate side-chains 218 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 68 MET Chi-restraints excluded: chain J residue 191 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 185 optimal weight: 0.2980 chunk 160 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 39 HIS ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17943 Z= 0.203 Angle : 0.573 9.776 24465 Z= 0.304 Chirality : 0.039 0.166 2687 Planarity : 0.004 0.111 2912 Dihedral : 17.286 165.512 2901 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.86 % Favored : 91.99 % Rotamer: Outliers : 2.23 % Allowed : 20.06 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1985 helix: 1.31 (0.18), residues: 891 sheet: -0.19 (0.34), residues: 254 loop : -2.09 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 165 HIS 0.005 0.001 HIS D 130 PHE 0.014 0.001 PHE C 340 TYR 0.011 0.001 TYR C 320 ARG 0.002 0.000 ARG B 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 1.769 Fit side-chains REVERT: A 313 MET cc_start: 0.7656 (ptp) cc_final: 0.7361 (mtm) REVERT: B 180 MET cc_start: 0.5814 (mpp) cc_final: 0.4300 (mmt) REVERT: D 126 MET cc_start: 0.7445 (tpp) cc_final: 0.6776 (tpp) REVERT: D 200 ASP cc_start: 0.6922 (m-30) cc_final: 0.6687 (p0) REVERT: D 305 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8368 (p) REVERT: D 342 TRP cc_start: 0.8403 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: E 62 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: I 68 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6052 (tpt) REVERT: J 68 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5304 (ttt) outliers start: 39 outliers final: 30 residues processed: 210 average time/residue: 0.2726 time to fit residues: 87.9574 Evaluate side-chains 215 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 TRP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 0 SER Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 68 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN D 215 ASN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.158843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123005 restraints weight = 23482.540| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.41 r_work: 0.3314 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17943 Z= 0.272 Angle : 0.607 8.467 24465 Z= 0.321 Chirality : 0.040 0.178 2687 Planarity : 0.005 0.111 2912 Dihedral : 17.363 166.448 2901 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.21 % Favored : 91.59 % Rotamer: Outliers : 2.51 % Allowed : 20.11 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 1985 helix: 1.22 (0.18), residues: 888 sheet: -0.29 (0.33), residues: 254 loop : -2.16 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 165 HIS 0.005 0.001 HIS D 130 PHE 0.019 0.001 PHE C 340 TYR 0.016 0.001 TYR C 320 ARG 0.003 0.000 ARG B 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.72 seconds wall clock time: 62 minutes 14.15 seconds (3734.15 seconds total)