Starting phenix.real_space_refine on Sat Mar 16 16:01:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpn_22416/03_2024/7jpn_22416_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpn_22416/03_2024/7jpn_22416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpn_22416/03_2024/7jpn_22416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpn_22416/03_2024/7jpn_22416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpn_22416/03_2024/7jpn_22416_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpn_22416/03_2024/7jpn_22416_updated.pdb" } resolution = 3.24 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= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 9562 2.51 5 N 2583 2.21 5 O 2809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 351": "OD1" <-> "OD2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 226": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15040 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3194 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2728 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2637 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2291 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1414 Classifications: {'peptide': 174} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 162} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1369 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1084 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 259 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.26, per 1000 atoms: 0.55 Number of scatterers: 15040 At special positions: 0 Unit cell: (93.632, 149.644, 134.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 6 15.00 Mg 2 11.99 O 2809 8.00 N 2583 7.00 C 9562 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: 5.93 Conformation dependent library (CDL) restraints added in 2.9 seconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 18 sheets defined 38.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.525A pdb=" N TRP A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.532A pdb=" N VAL A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 273 through 283 removed outlier: 4.028A pdb=" N GLY A 278 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 309 through 317 removed outlier: 4.587A pdb=" N ARG A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 331 through 354 Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.886A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 388 through 392' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 256 through 265 removed outlier: 3.923A pdb=" N GLU B 260 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA B 261 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Proline residue: B 262 - end of helix Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 291 through 300 removed outlier: 4.677A pdb=" N SER B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 353 through 364 Processing helix chain 'B' and resid 375 through 378 No H-bonds generated for 'chain 'B' and resid 375 through 378' Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.813A pdb=" N SER C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 64 through 70 removed outlier: 4.340A pdb=" N HIS D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 83 removed outlier: 7.642A pdb=" N SER D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 116 through 134 removed outlier: 4.065A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 190 removed outlier: 4.728A pdb=" N ARG D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 No H-bonds generated for 'chain 'D' and resid 207 through 210' Processing helix chain 'D' and resid 229 through 232 No H-bonds generated for 'chain 'D' and resid 229 through 232' Processing helix chain 'D' and resid 234 through 280 removed outlier: 4.639A pdb=" N ASP D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASN D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 246 " --> pdb=" O ASN D 242 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 52 removed outlier: 4.946A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 82 Processing helix chain 'E' and resid 88 through 100 Processing helix chain 'E' and resid 123 through 148 removed outlier: 4.012A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 removed outlier: 5.486A pdb=" N PHE E 163 " --> pdb=" O TRP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'F' and resid 6 through 19 Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 81 through 97 removed outlier: 3.882A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 128 through 167 removed outlier: 3.729A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 19 Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'G' and resid 51 through 58 Processing helix chain 'G' and resid 69 through 85 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 100 through 115 removed outlier: 4.004A pdb=" N GLU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 146 removed outlier: 3.647A pdb=" N GLN G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N GLY G 139 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 206 removed outlier: 4.454A pdb=" N GLN H 202 " --> pdb=" O ASN H 198 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS H 203 " --> pdb=" O ILE H 199 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N CYS H 204 " --> pdb=" O MET H 200 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER H 205 " --> pdb=" O ALA H 201 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 139 through 143 removed outlier: 6.747A pdb=" N PHE A 110 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 142 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 112 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS A 8 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR A 113 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL A 10 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 60 through 62 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.081A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 254 through 259 Processing sheet with id= E, first strand: chain 'B' and resid 30 through 33 removed outlier: 5.765A pdb=" N LYS B 106 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS B 11 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 108 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN B 13 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR B 110 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY B 135 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU B 109 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR B 137 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLU B 111 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ALA B 139 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 301 through 304 removed outlier: 6.077A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 242 through 245 Processing sheet with id= H, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.343A pdb=" N GLY C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.679A pdb=" N GLU C 36 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN C 44 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER C 38 " --> pdb=" O TRP C 42 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TRP C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 85 through 91 removed outlier: 3.807A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 131 through 137 removed outlier: 3.761A pdb=" N TRP C 131 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 126 " --> pdb=" O TRP C 131 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.664A pdb=" N GLY C 160 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU C 148 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA C 158 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP C 150 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU C 156 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 236 through 241 removed outlier: 3.838A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 207 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 247 through 252 removed outlier: 6.624A pdb=" N ALA C 261 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL C 250 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL C 259 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE C 252 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER C 257 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 283 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR C 271 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N PHE C 281 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP C 273 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU C 279 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 33 through 37 removed outlier: 3.757A pdb=" N VAL D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 142 through 144 Processing sheet with id= Q, first strand: chain 'E' and resid 14 through 16 removed outlier: 4.221A pdb=" N LYS E 14 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.774A pdb=" N LYS F 60 " --> pdb=" O ALA F 75 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1737 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: 4.34 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3151 1.33 - 1.45: 3499 1.45 - 1.57: 8594 1.57 - 1.69: 10 1.69 - 1.81: 119 Bond restraints: 15373 Sorted by residual: bond pdb=" N VAL A 393 " pdb=" CA VAL A 393 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.30e-03 1.16e+04 9.77e+00 bond pdb=" N GLU H 214 " pdb=" CA GLU H 214 " ideal model delta sigma weight residual 1.458 1.485 -0.027 9.00e-03 1.23e+04 9.02e+00 bond pdb=" N ILE H 212 " pdb=" CA ILE H 212 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.33e+00 bond pdb=" N HIS A 410 " pdb=" CA HIS A 410 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.22e-02 6.72e+03 7.72e+00 bond pdb=" N LYS H 203 " pdb=" CA LYS H 203 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.29e-02 6.01e+03 7.48e+00 ... (remaining 15368 not shown) Histogram of bond angle deviations from ideal: 98.72 - 106.96: 495 106.96 - 115.21: 9221 115.21 - 123.45: 10563 123.45 - 131.69: 496 131.69 - 139.94: 32 Bond angle restraints: 20807 Sorted by residual: angle pdb=" C ASN A 411 " pdb=" CA ASN A 411 " pdb=" CB ASN A 411 " ideal model delta sigma weight residual 110.17 118.22 -8.05 1.11e+00 8.12e-01 5.26e+01 angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 113.20 107.78 5.42 9.60e-01 1.09e+00 3.19e+01 angle pdb=" C TYR A 391 " pdb=" CA TYR A 391 " pdb=" CB TYR A 391 " ideal model delta sigma weight residual 110.63 121.04 -10.41 1.85e+00 2.92e-01 3.17e+01 angle pdb=" C ASN H 198 " pdb=" CA ASN H 198 " pdb=" CB ASN H 198 " ideal model delta sigma weight residual 110.85 120.14 -9.29 1.70e+00 3.46e-01 2.98e+01 angle pdb=" C ARG B 6 " pdb=" CA ARG B 6 " pdb=" CB ARG B 6 " ideal model delta sigma weight residual 115.79 110.30 5.49 1.19e+00 7.06e-01 2.13e+01 ... (remaining 20802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 8281 17.70 - 35.41: 786 35.41 - 53.11: 179 53.11 - 70.81: 30 70.81 - 88.52: 12 Dihedral angle restraints: 9288 sinusoidal: 3814 harmonic: 5474 Sorted by residual: dihedral pdb=" C ASN H 198 " pdb=" N ASN H 198 " pdb=" CA ASN H 198 " pdb=" CB ASN H 198 " ideal model delta harmonic sigma weight residual -122.60 -138.83 16.23 0 2.50e+00 1.60e-01 4.21e+01 dihedral pdb=" N ASN H 198 " pdb=" C ASN H 198 " pdb=" CA ASN H 198 " pdb=" CB ASN H 198 " ideal model delta harmonic sigma weight residual 122.80 136.15 -13.35 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" C TYR A 391 " pdb=" N TYR A 391 " pdb=" CA TYR A 391 " pdb=" CB TYR A 391 " ideal model delta harmonic sigma weight residual -122.60 -133.23 10.63 0 2.50e+00 1.60e-01 1.81e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2221 0.113 - 0.225: 54 0.225 - 0.338: 4 0.338 - 0.450: 1 0.450 - 0.563: 1 Chirality restraints: 2281 Sorted by residual: chirality pdb=" CA ASN H 198 " pdb=" N ASN H 198 " pdb=" C ASN H 198 " pdb=" CB ASN H 198 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" CA ASP H 217 " pdb=" N ASP H 217 " pdb=" C ASP H 217 " pdb=" CB ASP H 217 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB ILE E 16 " pdb=" CA ILE E 16 " pdb=" CG1 ILE E 16 " pdb=" CG2 ILE E 16 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2278 not shown) Planarity restraints: 2674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 224 " 0.037 2.00e-02 2.50e+03 1.80e-02 8.12e+00 pdb=" CG TRP H 224 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP H 224 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 224 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP H 224 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 224 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 224 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 224 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 224 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 224 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 386 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C SER A 386 " 0.035 2.00e-02 2.50e+03 pdb=" O SER A 386 " -0.013 2.00e-02 2.50e+03 pdb=" N THR A 387 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 151 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.69e+00 pdb=" N PRO C 152 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " -0.027 5.00e-02 4.00e+02 ... (remaining 2671 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 89 2.52 - 3.11: 11058 3.11 - 3.71: 23756 3.71 - 4.30: 34288 4.30 - 4.90: 57045 Nonbonded interactions: 126236 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O2B ATP A 502 " model vdw 1.919 2.170 nonbonded pdb=" NH1 ARG B 214 " pdb=" OE2 GLU B 218 " model vdw 2.104 2.520 nonbonded pdb=" OG SER C 170 " pdb=" O PRO C 190 " model vdw 2.114 2.440 nonbonded pdb=" OH TYR A 233 " pdb=" OE1 GLU A 241 " model vdw 2.185 2.440 nonbonded pdb=" OD1 ASP B 158 " pdb="MG MG B 501 " model vdw 2.198 2.170 ... (remaining 126231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.640 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: 7.500 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 42.290 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.004 0.056 15373 Z= 0.238 Angle : 0.632 10.409 20807 Z= 0.371 Chirality : 0.049 0.563 2281 Planarity : 0.004 0.048 2674 Dihedral : 14.752 88.518 5756 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.55 % Allowed : 0.92 % Favored : 98.52 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.19 % 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: 0.43 (0.20), residues: 1863 helix: 1.14 (0.20), residues: 694 sheet: -0.36 (0.27), residues: 361 loop : -0.01 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 224 HIS 0.005 0.001 HIS D 254 PHE 0.029 0.002 PHE A 283 TYR 0.029 0.002 TYR A 125 ARG 0.009 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 489 time to evaluate : 1.672 Fit side-chains REVERT: A 93 MET cc_start: 0.7210 (tpp) cc_final: 0.7009 (tpp) REVERT: A 188 SER cc_start: 0.8346 (p) cc_final: 0.8084 (m) REVERT: A 205 GLN cc_start: 0.7583 (tt0) cc_final: 0.7332 (tt0) REVERT: A 237 ASP cc_start: 0.6549 (t70) cc_final: 0.6281 (t70) REVERT: A 255 GLN cc_start: 0.8618 (mp10) cc_final: 0.8412 (mm-40) REVERT: A 274 GLU cc_start: 0.6665 (pm20) cc_final: 0.6114 (pm20) REVERT: A 292 PHE cc_start: 0.7624 (t80) cc_final: 0.7048 (t80) REVERT: A 333 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7198 (tpp80) REVERT: A 338 ASP cc_start: 0.6751 (m-30) cc_final: 0.6549 (m-30) REVERT: A 344 ASP cc_start: 0.7409 (m-30) cc_final: 0.7184 (m-30) REVERT: A 368 ILE cc_start: 0.8144 (mm) cc_final: 0.7930 (mm) REVERT: B 74 MET cc_start: 0.0246 (mmp) cc_final: -0.0024 (mmp) REVERT: B 85 MET cc_start: 0.7601 (mmp) cc_final: 0.7196 (mmp) REVERT: B 115 ASN cc_start: 0.7828 (t0) cc_final: 0.7571 (t0) REVERT: B 127 MET cc_start: 0.7141 (mmp) cc_final: 0.6871 (mmp) REVERT: B 140 ILE cc_start: 0.8018 (mt) cc_final: 0.7804 (mt) REVERT: B 257 GLU cc_start: 0.7223 (mp0) cc_final: 0.6930 (mp0) REVERT: B 260 GLU cc_start: 0.6917 (mp0) cc_final: 0.6574 (mp0) REVERT: C 64 SER cc_start: 0.8503 (m) cc_final: 0.8268 (m) REVERT: C 92 ILE cc_start: 0.8133 (pt) cc_final: 0.7314 (pt) REVERT: C 102 VAL cc_start: 0.7970 (p) cc_final: 0.7558 (t) REVERT: C 178 GLU cc_start: 0.7052 (pm20) cc_final: 0.6778 (pm20) REVERT: C 225 THR cc_start: 0.8241 (p) cc_final: 0.8020 (p) REVERT: D 5 GLU cc_start: 0.6990 (pm20) cc_final: 0.6630 (pm20) REVERT: D 65 LYS cc_start: 0.7891 (mttp) cc_final: 0.7639 (mttp) REVERT: D 74 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6690 (tm-30) REVERT: D 106 LYS cc_start: 0.8187 (mppt) cc_final: 0.7929 (mppt) REVERT: D 119 ASN cc_start: 0.8014 (m110) cc_final: 0.7696 (m-40) REVERT: D 186 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7805 (ttmm) REVERT: D 204 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6751 (mm-30) REVERT: E 14 LYS cc_start: 0.7766 (mptt) cc_final: 0.7514 (mptt) REVERT: E 63 GLU cc_start: 0.7579 (mp0) cc_final: 0.7179 (mp0) REVERT: E 80 LYS cc_start: 0.7488 (mttp) cc_final: 0.7199 (mttp) REVERT: E 88 LYS cc_start: 0.8216 (tmmt) cc_final: 0.7938 (tmmt) REVERT: F 39 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6836 (mm-30) REVERT: F 45 GLU cc_start: 0.7776 (pm20) cc_final: 0.7473 (pm20) REVERT: F 141 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6358 (mm-30) REVERT: F 163 GLU cc_start: 0.6999 (tp30) cc_final: 0.6430 (tp30) REVERT: F 167 ASN cc_start: 0.7235 (m110) cc_final: 0.7016 (m-40) REVERT: G 107 MET cc_start: 0.7442 (tpp) cc_final: 0.7070 (tpp) outliers start: 9 outliers final: 3 residues processed: 497 average time/residue: 0.3572 time to fit residues: 237.2709 Evaluate side-chains 478 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 475 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 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 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 366 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS F 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15373 Z= 0.310 Angle : 0.538 8.130 20807 Z= 0.282 Chirality : 0.046 0.202 2281 Planarity : 0.004 0.050 2674 Dihedral : 7.040 89.832 2117 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.17 % Allowed : 8.97 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.54 (0.20), residues: 1863 helix: 1.30 (0.20), residues: 695 sheet: -0.28 (0.27), residues: 356 loop : -0.04 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 224 HIS 0.006 0.001 HIS F 137 PHE 0.022 0.002 PHE B 340 TYR 0.023 0.002 TYR A 125 ARG 0.011 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 474 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7624 (tt0) cc_final: 0.7387 (tt0) REVERT: A 188 SER cc_start: 0.8336 (p) cc_final: 0.8086 (m) REVERT: A 205 GLN cc_start: 0.7596 (tt0) cc_final: 0.7325 (tt0) REVERT: A 209 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.7047 (mtm-85) REVERT: A 221 LEU cc_start: 0.8449 (tp) cc_final: 0.8223 (tp) REVERT: A 237 ASP cc_start: 0.6431 (t70) cc_final: 0.6215 (t70) REVERT: A 255 GLN cc_start: 0.8603 (mp10) cc_final: 0.8370 (mm-40) REVERT: A 274 GLU cc_start: 0.6666 (pm20) cc_final: 0.6133 (pm20) REVERT: A 292 PHE cc_start: 0.7700 (t80) cc_final: 0.7101 (t80) REVERT: A 317 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7894 (ttmm) REVERT: A 333 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7583 (ttm-80) REVERT: A 338 ASP cc_start: 0.6781 (m-30) cc_final: 0.6524 (m-30) REVERT: B 74 MET cc_start: 0.0235 (mmp) cc_final: -0.0069 (mmp) REVERT: B 85 MET cc_start: 0.7624 (mmp) cc_final: 0.7268 (mmp) REVERT: B 127 MET cc_start: 0.7187 (mmp) cc_final: 0.6928 (mmp) REVERT: B 140 ILE cc_start: 0.8074 (mt) cc_final: 0.7836 (mt) REVERT: B 145 THR cc_start: 0.8342 (m) cc_final: 0.8043 (m) REVERT: B 179 THR cc_start: 0.8344 (m) cc_final: 0.8112 (t) REVERT: B 214 ARG cc_start: 0.7597 (ttp80) cc_final: 0.6983 (ttp80) REVERT: B 257 GLU cc_start: 0.7269 (mp0) cc_final: 0.7036 (mp0) REVERT: B 260 GLU cc_start: 0.7067 (mp0) cc_final: 0.6489 (mp0) REVERT: C 92 ILE cc_start: 0.8128 (pt) cc_final: 0.7809 (pt) REVERT: C 102 VAL cc_start: 0.8055 (p) cc_final: 0.7655 (t) REVERT: C 178 GLU cc_start: 0.7062 (pm20) cc_final: 0.6769 (pm20) REVERT: C 195 MET cc_start: 0.7750 (mmm) cc_final: 0.7205 (mmm) REVERT: C 326 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8201 (mmmt) REVERT: D 5 GLU cc_start: 0.6939 (pm20) cc_final: 0.6597 (pm20) REVERT: D 65 LYS cc_start: 0.7899 (mttp) cc_final: 0.7644 (mttp) REVERT: D 74 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6628 (tm-30) REVERT: D 106 LYS cc_start: 0.8244 (mppt) cc_final: 0.7983 (mppt) REVERT: D 115 MET cc_start: 0.6763 (mtm) cc_final: 0.6368 (mtt) REVERT: D 119 ASN cc_start: 0.8141 (m110) cc_final: 0.7730 (m-40) REVERT: D 155 GLU cc_start: 0.6942 (tt0) cc_final: 0.6697 (tt0) REVERT: D 166 SER cc_start: 0.7938 (m) cc_final: 0.7657 (t) REVERT: D 186 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7798 (ttmm) REVERT: D 204 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6872 (mm-30) REVERT: D 281 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7864 (mtt90) REVERT: E 14 LYS cc_start: 0.7771 (mptt) cc_final: 0.7507 (mptt) REVERT: E 63 GLU cc_start: 0.7654 (mp0) cc_final: 0.7348 (mp0) REVERT: E 80 LYS cc_start: 0.7633 (mttp) cc_final: 0.7407 (mttp) REVERT: E 88 LYS cc_start: 0.8246 (tmmt) cc_final: 0.7936 (tmmt) REVERT: F 39 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6753 (mm-30) REVERT: F 45 GLU cc_start: 0.7773 (pm20) cc_final: 0.7430 (pm20) REVERT: F 94 MET cc_start: 0.7877 (mtp) cc_final: 0.7676 (mtm) REVERT: F 141 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6376 (mm-30) REVERT: F 163 GLU cc_start: 0.6999 (tp30) cc_final: 0.6415 (tp30) REVERT: F 167 ASN cc_start: 0.7351 (m110) cc_final: 0.7106 (m-40) REVERT: H 222 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6851 (mm-30) outliers start: 19 outliers final: 9 residues processed: 479 average time/residue: 0.3667 time to fit residues: 234.4502 Evaluate side-chains 476 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 467 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN C 30 HIS D 140 ASN D 245 HIS F 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15373 Z= 0.214 Angle : 0.502 9.794 20807 Z= 0.263 Chirality : 0.044 0.178 2281 Planarity : 0.004 0.049 2674 Dihedral : 6.378 86.671 2115 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.54 % Allowed : 11.43 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.67 (0.20), residues: 1863 helix: 1.45 (0.20), residues: 694 sheet: -0.20 (0.28), residues: 347 loop : -0.01 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 131 HIS 0.004 0.001 HIS F 137 PHE 0.019 0.002 PHE A 276 TYR 0.026 0.002 TYR E 74 ARG 0.006 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 474 time to evaluate : 1.799 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7097 (mtm-85) cc_final: 0.6761 (mtm-85) REVERT: A 93 MET cc_start: 0.7331 (mmm) cc_final: 0.7067 (mmm) REVERT: A 188 SER cc_start: 0.8310 (p) cc_final: 0.8067 (m) REVERT: A 205 GLN cc_start: 0.7511 (tt0) cc_final: 0.7152 (tt0) REVERT: A 209 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.7021 (mtm-85) REVERT: A 221 LEU cc_start: 0.8434 (tp) cc_final: 0.8165 (tp) REVERT: A 237 ASP cc_start: 0.6428 (t70) cc_final: 0.6219 (t70) REVERT: A 255 GLN cc_start: 0.8610 (mp10) cc_final: 0.8348 (mm-40) REVERT: A 267 PHE cc_start: 0.8066 (p90) cc_final: 0.7757 (p90) REVERT: A 274 GLU cc_start: 0.6620 (pm20) cc_final: 0.6060 (pm20) REVERT: A 292 PHE cc_start: 0.7706 (t80) cc_final: 0.7099 (t80) REVERT: A 317 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7956 (ttmm) REVERT: A 338 ASP cc_start: 0.6788 (m-30) cc_final: 0.6503 (m-30) REVERT: A 386 SER cc_start: 0.8363 (t) cc_final: 0.8111 (t) REVERT: B 74 MET cc_start: 0.0184 (mmp) cc_final: -0.0183 (mmp) REVERT: B 85 MET cc_start: 0.7644 (mmp) cc_final: 0.7227 (mmp) REVERT: B 127 MET cc_start: 0.7157 (mmp) cc_final: 0.6944 (mmp) REVERT: B 140 ILE cc_start: 0.8027 (mt) cc_final: 0.7820 (mt) REVERT: B 260 GLU cc_start: 0.7083 (mp0) cc_final: 0.6449 (mp0) REVERT: B 325 TYR cc_start: 0.8400 (t80) cc_final: 0.8182 (t80) REVERT: B 340 PHE cc_start: 0.8048 (t80) cc_final: 0.7714 (t80) REVERT: B 365 MET cc_start: 0.4704 (ppp) cc_final: 0.4364 (ppp) REVERT: C 58 ILE cc_start: 0.8182 (mt) cc_final: 0.7903 (tt) REVERT: C 70 CYS cc_start: 0.7702 (p) cc_final: 0.7389 (p) REVERT: C 79 TRP cc_start: 0.8752 (m100) cc_final: 0.8414 (m100) REVERT: C 102 VAL cc_start: 0.8069 (p) cc_final: 0.7425 (t) REVERT: C 110 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7900 (mtmm) REVERT: C 195 MET cc_start: 0.7747 (mmm) cc_final: 0.7215 (mmm) REVERT: C 326 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8161 (mmmt) REVERT: D 5 GLU cc_start: 0.6886 (pm20) cc_final: 0.6529 (pm20) REVERT: D 65 LYS cc_start: 0.7886 (mttp) cc_final: 0.7628 (mttp) REVERT: D 74 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6594 (tm-30) REVERT: D 106 LYS cc_start: 0.8280 (mppt) cc_final: 0.7996 (mppt) REVERT: D 115 MET cc_start: 0.6873 (mtm) cc_final: 0.6465 (mtm) REVERT: D 119 ASN cc_start: 0.8169 (m110) cc_final: 0.7710 (m-40) REVERT: D 155 GLU cc_start: 0.6920 (tt0) cc_final: 0.6664 (tt0) REVERT: D 166 SER cc_start: 0.7955 (m) cc_final: 0.7660 (t) REVERT: D 186 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7772 (ttmm) REVERT: D 204 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6848 (mm-30) REVERT: D 266 MET cc_start: 0.7622 (mtt) cc_final: 0.7322 (mtp) REVERT: D 281 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7838 (mtt90) REVERT: E 14 LYS cc_start: 0.7765 (mptt) cc_final: 0.7505 (mptt) REVERT: E 80 LYS cc_start: 0.7588 (mttp) cc_final: 0.7378 (mttp) REVERT: E 88 LYS cc_start: 0.8249 (tmmt) cc_final: 0.7907 (tmmt) REVERT: F 39 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6752 (mm-30) REVERT: F 45 GLU cc_start: 0.7769 (pm20) cc_final: 0.7437 (pm20) REVERT: F 141 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6315 (mm-30) REVERT: F 163 GLU cc_start: 0.6994 (tp30) cc_final: 0.6404 (tp30) REVERT: F 167 ASN cc_start: 0.7295 (m110) cc_final: 0.7040 (m-40) outliers start: 25 outliers final: 16 residues processed: 480 average time/residue: 0.3674 time to fit residues: 236.4904 Evaluate side-chains 480 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 464 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 167 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 245 HIS ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15373 Z= 0.241 Angle : 0.505 10.525 20807 Z= 0.265 Chirality : 0.044 0.171 2281 Planarity : 0.004 0.050 2674 Dihedral : 6.271 87.622 2115 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.66 % Allowed : 13.09 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.67 (0.20), residues: 1863 helix: 1.51 (0.20), residues: 687 sheet: -0.21 (0.28), residues: 344 loop : -0.06 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 224 HIS 0.006 0.001 HIS D 245 PHE 0.023 0.002 PHE B 355 TYR 0.030 0.001 TYR E 74 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 474 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7120 (mtm-85) cc_final: 0.6744 (mtm-85) REVERT: A 93 MET cc_start: 0.7383 (mmm) cc_final: 0.7112 (mmm) REVERT: A 188 SER cc_start: 0.8328 (p) cc_final: 0.8074 (m) REVERT: A 205 GLN cc_start: 0.7515 (tt0) cc_final: 0.7240 (tt0) REVERT: A 221 LEU cc_start: 0.8437 (tp) cc_final: 0.8157 (tp) REVERT: A 237 ASP cc_start: 0.6459 (t70) cc_final: 0.6228 (t70) REVERT: A 255 GLN cc_start: 0.8610 (mp10) cc_final: 0.8358 (mm-40) REVERT: A 267 PHE cc_start: 0.8146 (p90) cc_final: 0.7749 (p90) REVERT: A 274 GLU cc_start: 0.6562 (pm20) cc_final: 0.6027 (pm20) REVERT: A 292 PHE cc_start: 0.7724 (t80) cc_final: 0.7106 (t80) REVERT: A 317 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7991 (ttmm) REVERT: A 338 ASP cc_start: 0.6765 (m-30) cc_final: 0.6501 (m-30) REVERT: A 386 SER cc_start: 0.8332 (t) cc_final: 0.8120 (t) REVERT: B 74 MET cc_start: 0.0007 (mmp) cc_final: -0.0366 (mmp) REVERT: B 85 MET cc_start: 0.7617 (mmp) cc_final: 0.7209 (mmp) REVERT: B 127 MET cc_start: 0.7229 (mmp) cc_final: 0.7010 (mmp) REVERT: B 140 ILE cc_start: 0.8060 (mt) cc_final: 0.7844 (mt) REVERT: B 260 GLU cc_start: 0.7123 (mp0) cc_final: 0.6483 (mp0) REVERT: B 339 LYS cc_start: 0.8439 (mptt) cc_final: 0.8190 (mptt) REVERT: B 350 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7858 (ttm170) REVERT: B 365 MET cc_start: 0.4719 (ppp) cc_final: 0.4301 (ppp) REVERT: C 58 ILE cc_start: 0.8184 (mt) cc_final: 0.7928 (tt) REVERT: C 70 CYS cc_start: 0.7714 (p) cc_final: 0.7351 (p) REVERT: C 79 TRP cc_start: 0.8739 (m100) cc_final: 0.8438 (m100) REVERT: C 102 VAL cc_start: 0.8083 (p) cc_final: 0.7453 (t) REVERT: C 110 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7999 (mtmm) REVERT: C 195 MET cc_start: 0.7763 (mmm) cc_final: 0.7235 (mmm) REVERT: C 326 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8147 (mmmt) REVERT: D 5 GLU cc_start: 0.6874 (pm20) cc_final: 0.6531 (pm20) REVERT: D 65 LYS cc_start: 0.7872 (mttp) cc_final: 0.7606 (mttp) REVERT: D 74 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6598 (tm-30) REVERT: D 106 LYS cc_start: 0.8278 (mppt) cc_final: 0.8000 (mppt) REVERT: D 115 MET cc_start: 0.6981 (mtm) cc_final: 0.6546 (mtm) REVERT: D 119 ASN cc_start: 0.8182 (m110) cc_final: 0.7731 (m-40) REVERT: D 155 GLU cc_start: 0.6940 (tt0) cc_final: 0.6682 (tt0) REVERT: D 166 SER cc_start: 0.8017 (m) cc_final: 0.7722 (t) REVERT: D 186 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7778 (ttmm) REVERT: D 204 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6875 (mm-30) REVERT: D 266 MET cc_start: 0.7623 (mtt) cc_final: 0.7351 (mtp) REVERT: D 281 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7790 (mtt90) REVERT: E 14 LYS cc_start: 0.7772 (mptt) cc_final: 0.7513 (mptt) REVERT: E 19 MET cc_start: 0.7142 (mmm) cc_final: 0.6871 (tpt) REVERT: E 80 LYS cc_start: 0.7588 (mttp) cc_final: 0.7383 (mttp) REVERT: E 88 LYS cc_start: 0.8255 (tmmt) cc_final: 0.7911 (tmmt) REVERT: F 39 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6785 (mm-30) REVERT: F 70 VAL cc_start: 0.8438 (p) cc_final: 0.8203 (t) REVERT: F 141 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6320 (mm-30) REVERT: F 163 GLU cc_start: 0.6997 (tp30) cc_final: 0.6411 (tp30) REVERT: F 167 ASN cc_start: 0.7313 (m110) cc_final: 0.7052 (m-40) REVERT: G 51 MET cc_start: 0.7000 (tpp) cc_final: 0.6759 (mpp) outliers start: 27 outliers final: 19 residues processed: 480 average time/residue: 0.3741 time to fit residues: 239.9834 Evaluate side-chains 484 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 465 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 2 optimal weight: 0.0030 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 145 HIS ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15373 Z= 0.189 Angle : 0.492 10.664 20807 Z= 0.259 Chirality : 0.043 0.162 2281 Planarity : 0.004 0.049 2674 Dihedral : 6.137 89.145 2115 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.72 % Allowed : 14.87 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.70 (0.20), residues: 1863 helix: 1.56 (0.20), residues: 686 sheet: -0.27 (0.28), residues: 353 loop : -0.02 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 224 HIS 0.005 0.001 HIS C 206 PHE 0.017 0.001 PHE A 276 TYR 0.035 0.001 TYR E 74 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 470 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6726 (mtm-85) REVERT: A 188 SER cc_start: 0.8305 (p) cc_final: 0.8064 (m) REVERT: A 205 GLN cc_start: 0.7444 (tt0) cc_final: 0.7218 (tt0) REVERT: A 221 LEU cc_start: 0.8427 (tp) cc_final: 0.8195 (tp) REVERT: A 237 ASP cc_start: 0.6455 (t70) cc_final: 0.6173 (t70) REVERT: A 255 GLN cc_start: 0.8614 (mp10) cc_final: 0.8342 (mm-40) REVERT: A 267 PHE cc_start: 0.8160 (p90) cc_final: 0.7735 (p90) REVERT: A 274 GLU cc_start: 0.6525 (pm20) cc_final: 0.6028 (pm20) REVERT: A 292 PHE cc_start: 0.7713 (t80) cc_final: 0.7119 (t80) REVERT: A 317 LYS cc_start: 0.8234 (mtmm) cc_final: 0.8011 (ttmm) REVERT: A 338 ASP cc_start: 0.6753 (m-30) cc_final: 0.6496 (m-30) REVERT: A 386 SER cc_start: 0.8295 (t) cc_final: 0.8093 (t) REVERT: B 74 MET cc_start: -0.0121 (mmp) cc_final: -0.0399 (mmp) REVERT: B 85 MET cc_start: 0.7604 (mmp) cc_final: 0.7209 (mmp) REVERT: B 122 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7609 (tmtt) REVERT: B 214 ARG cc_start: 0.7573 (ttp80) cc_final: 0.7342 (ttp80) REVERT: B 260 GLU cc_start: 0.7120 (mp0) cc_final: 0.6487 (mp0) REVERT: B 350 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7825 (ttm170) REVERT: B 365 MET cc_start: 0.4664 (ppp) cc_final: 0.4209 (ppp) REVERT: C 58 ILE cc_start: 0.8158 (mt) cc_final: 0.7915 (tt) REVERT: C 70 CYS cc_start: 0.7692 (p) cc_final: 0.7313 (p) REVERT: C 74 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8141 (mtp180) REVERT: C 79 TRP cc_start: 0.8709 (m100) cc_final: 0.8420 (m100) REVERT: C 82 LYS cc_start: 0.7691 (tptt) cc_final: 0.7487 (tptt) REVERT: C 102 VAL cc_start: 0.8086 (p) cc_final: 0.7439 (t) REVERT: C 110 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7713 (pttm) REVERT: C 195 MET cc_start: 0.7756 (mmm) cc_final: 0.7236 (mmm) REVERT: C 326 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8118 (mmmt) REVERT: D 5 GLU cc_start: 0.6840 (pm20) cc_final: 0.6515 (pm20) REVERT: D 65 LYS cc_start: 0.7879 (mttp) cc_final: 0.7614 (mttp) REVERT: D 74 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6599 (tm-30) REVERT: D 92 ASN cc_start: 0.8577 (m110) cc_final: 0.8361 (m-40) REVERT: D 106 LYS cc_start: 0.8282 (mppt) cc_final: 0.8010 (mppt) REVERT: D 155 GLU cc_start: 0.6923 (tt0) cc_final: 0.6667 (tt0) REVERT: D 166 SER cc_start: 0.8043 (m) cc_final: 0.7738 (t) REVERT: D 186 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7763 (ttmm) REVERT: D 204 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6854 (mm-30) REVERT: E 14 LYS cc_start: 0.7762 (mptt) cc_final: 0.7489 (mptt) REVERT: E 88 LYS cc_start: 0.8211 (tmmt) cc_final: 0.7890 (tmmt) REVERT: F 39 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6789 (mm-30) REVERT: F 70 VAL cc_start: 0.8439 (p) cc_final: 0.8225 (t) REVERT: F 141 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6312 (mm-30) REVERT: F 163 GLU cc_start: 0.6985 (tp30) cc_final: 0.6411 (tp30) REVERT: F 167 ASN cc_start: 0.7233 (m110) cc_final: 0.6992 (m-40) REVERT: G 51 MET cc_start: 0.6990 (tpp) cc_final: 0.6755 (mpp) outliers start: 28 outliers final: 21 residues processed: 479 average time/residue: 0.3503 time to fit residues: 224.6834 Evaluate side-chains 488 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 466 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 35 optimal weight: 0.0050 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 178 optimal weight: 0.0980 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 58 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS D 140 ASN D 245 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15373 Z= 0.141 Angle : 0.483 10.506 20807 Z= 0.253 Chirality : 0.043 0.159 2281 Planarity : 0.004 0.047 2674 Dihedral : 5.932 89.928 2115 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.09 % Allowed : 15.49 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.80 (0.20), residues: 1863 helix: 1.61 (0.20), residues: 687 sheet: -0.16 (0.28), residues: 351 loop : 0.04 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 131 HIS 0.004 0.001 HIS C 206 PHE 0.016 0.001 PHE A 276 TYR 0.036 0.001 TYR E 74 ARG 0.007 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 457 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6699 (mtm-85) REVERT: A 221 LEU cc_start: 0.8444 (tp) cc_final: 0.8236 (tp) REVERT: A 255 GLN cc_start: 0.8632 (mp10) cc_final: 0.8381 (mm-40) REVERT: A 267 PHE cc_start: 0.8170 (p90) cc_final: 0.7708 (p90) REVERT: A 274 GLU cc_start: 0.6460 (pm20) cc_final: 0.5942 (pm20) REVERT: A 276 PHE cc_start: 0.7867 (p90) cc_final: 0.7559 (p90) REVERT: A 292 PHE cc_start: 0.7685 (t80) cc_final: 0.7066 (t80) REVERT: A 317 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7854 (ttmm) REVERT: A 333 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7160 (ttp80) REVERT: A 338 ASP cc_start: 0.6751 (m-30) cc_final: 0.6507 (m-30) REVERT: B 85 MET cc_start: 0.7595 (mmp) cc_final: 0.7174 (mmp) REVERT: B 114 MET cc_start: 0.7587 (mmm) cc_final: 0.7207 (mmm) REVERT: B 122 LYS cc_start: 0.8026 (tmtt) cc_final: 0.7583 (tmtt) REVERT: B 260 GLU cc_start: 0.7087 (mp0) cc_final: 0.6529 (mp0) REVERT: B 350 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7772 (ttm170) REVERT: B 365 MET cc_start: 0.4747 (ppp) cc_final: 0.4280 (ppp) REVERT: C 70 CYS cc_start: 0.7653 (p) cc_final: 0.7281 (p) REVERT: C 74 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8138 (mtp180) REVERT: C 79 TRP cc_start: 0.8679 (m100) cc_final: 0.8433 (m100) REVERT: C 82 LYS cc_start: 0.7754 (tptt) cc_final: 0.7547 (tptt) REVERT: C 102 VAL cc_start: 0.8071 (p) cc_final: 0.7401 (t) REVERT: C 195 MET cc_start: 0.7695 (mmm) cc_final: 0.7282 (mmm) REVERT: C 198 SER cc_start: 0.6935 (p) cc_final: 0.6729 (t) REVERT: C 326 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8089 (mmmt) REVERT: D 13 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5839 (mp0) REVERT: D 65 LYS cc_start: 0.7887 (mttp) cc_final: 0.7620 (mttp) REVERT: D 74 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6637 (tm-30) REVERT: D 106 LYS cc_start: 0.8276 (mppt) cc_final: 0.8000 (mppt) REVERT: D 155 GLU cc_start: 0.6866 (tt0) cc_final: 0.6601 (tt0) REVERT: D 166 SER cc_start: 0.8042 (m) cc_final: 0.7730 (t) REVERT: D 186 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7753 (ttmm) REVERT: D 204 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6825 (mm-30) REVERT: E 80 LYS cc_start: 0.7363 (mttp) cc_final: 0.6819 (mtmp) REVERT: F 39 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6738 (mm-30) REVERT: F 70 VAL cc_start: 0.8498 (p) cc_final: 0.8254 (t) REVERT: F 110 GLU cc_start: 0.7200 (mp0) cc_final: 0.6883 (mp0) REVERT: F 139 MET cc_start: 0.8215 (mtp) cc_final: 0.7958 (mtp) REVERT: F 141 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6292 (mm-30) REVERT: F 163 GLU cc_start: 0.6969 (tp30) cc_final: 0.6485 (tp30) REVERT: F 167 ASN cc_start: 0.7273 (m110) cc_final: 0.6986 (m-40) REVERT: G 51 MET cc_start: 0.6947 (tpp) cc_final: 0.6714 (mpp) REVERT: H 196 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7831 (p) outliers start: 34 outliers final: 22 residues processed: 470 average time/residue: 0.3670 time to fit residues: 233.8625 Evaluate side-chains 476 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 451 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 0.0370 chunk 177 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 81 optimal weight: 0.0020 overall best weight: 0.3066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 245 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 15373 Z= 0.155 Angle : 0.485 10.421 20807 Z= 0.253 Chirality : 0.042 0.153 2281 Planarity : 0.004 0.046 2674 Dihedral : 5.838 88.214 2115 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.09 % Allowed : 16.04 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.85 (0.20), residues: 1863 helix: 1.64 (0.20), residues: 688 sheet: -0.13 (0.28), residues: 351 loop : 0.08 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 131 HIS 0.009 0.001 HIS D 245 PHE 0.015 0.001 PHE A 276 TYR 0.041 0.001 TYR E 74 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 454 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7099 (mtm-85) cc_final: 0.6767 (mtm-85) REVERT: A 93 MET cc_start: 0.7331 (mmm) cc_final: 0.7091 (mmm) REVERT: A 255 GLN cc_start: 0.8625 (mp10) cc_final: 0.8376 (mm-40) REVERT: A 267 PHE cc_start: 0.8195 (p90) cc_final: 0.7706 (p90) REVERT: A 274 GLU cc_start: 0.6439 (pm20) cc_final: 0.5936 (pm20) REVERT: A 276 PHE cc_start: 0.7851 (p90) cc_final: 0.7554 (p90) REVERT: A 292 PHE cc_start: 0.7677 (t80) cc_final: 0.7055 (t80) REVERT: A 317 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7877 (ttmm) REVERT: A 333 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7188 (ttp80) REVERT: A 338 ASP cc_start: 0.6761 (m-30) cc_final: 0.6523 (m-30) REVERT: B 114 MET cc_start: 0.7492 (mmm) cc_final: 0.7102 (mmm) REVERT: B 122 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7595 (tmtt) REVERT: B 127 MET cc_start: 0.7028 (mmp) cc_final: 0.6795 (mmp) REVERT: B 233 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7853 (mp) REVERT: B 260 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: B 365 MET cc_start: 0.4818 (ppp) cc_final: 0.4308 (ppp) REVERT: C 67 ILE cc_start: 0.8281 (mt) cc_final: 0.7936 (tt) REVERT: C 70 CYS cc_start: 0.7613 (p) cc_final: 0.7185 (p) REVERT: C 74 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8136 (mtp180) REVERT: C 79 TRP cc_start: 0.8681 (m100) cc_final: 0.8419 (m100) REVERT: C 102 VAL cc_start: 0.8075 (p) cc_final: 0.7426 (t) REVERT: C 195 MET cc_start: 0.7682 (mmm) cc_final: 0.7305 (mmm) REVERT: C 326 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8068 (mmmt) REVERT: D 65 LYS cc_start: 0.7874 (mttp) cc_final: 0.7621 (mttp) REVERT: D 74 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6641 (tm-30) REVERT: D 106 LYS cc_start: 0.8273 (mppt) cc_final: 0.8004 (mppt) REVERT: D 126 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6780 (mm-30) REVERT: D 155 GLU cc_start: 0.6855 (tt0) cc_final: 0.6590 (tt0) REVERT: D 166 SER cc_start: 0.8087 (m) cc_final: 0.7792 (t) REVERT: D 186 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7750 (ttmm) REVERT: D 204 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6802 (mm-30) REVERT: E 80 LYS cc_start: 0.7393 (mttp) cc_final: 0.6858 (mtmp) REVERT: E 129 MET cc_start: 0.7072 (ttm) cc_final: 0.6871 (ttm) REVERT: F 39 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6752 (mm-30) REVERT: F 70 VAL cc_start: 0.8504 (p) cc_final: 0.8263 (t) REVERT: F 110 GLU cc_start: 0.7203 (mp0) cc_final: 0.6880 (mp0) REVERT: F 141 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6304 (mm-30) REVERT: F 163 GLU cc_start: 0.6959 (tp30) cc_final: 0.6479 (tp30) REVERT: F 167 ASN cc_start: 0.7286 (m110) cc_final: 0.6989 (m-40) REVERT: G 51 MET cc_start: 0.6960 (tpp) cc_final: 0.6726 (mpp) outliers start: 34 outliers final: 25 residues processed: 467 average time/residue: 0.3633 time to fit residues: 227.4396 Evaluate side-chains 477 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 449 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15373 Z= 0.329 Angle : 0.548 10.889 20807 Z= 0.285 Chirality : 0.045 0.152 2281 Planarity : 0.004 0.047 2674 Dihedral : 6.024 89.305 2114 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.27 % Allowed : 16.59 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.74 (0.20), residues: 1863 helix: 1.53 (0.20), residues: 689 sheet: -0.18 (0.28), residues: 351 loop : 0.02 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 224 HIS 0.013 0.001 HIS D 245 PHE 0.038 0.002 PHE B 340 TYR 0.054 0.002 TYR B 325 ARG 0.009 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 468 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7141 (mtm-85) cc_final: 0.6832 (mtm-85) REVERT: A 161 ARG cc_start: 0.7975 (mtt90) cc_final: 0.7683 (mtm180) REVERT: A 237 ASP cc_start: 0.6623 (t70) cc_final: 0.6356 (t70) REVERT: A 255 GLN cc_start: 0.8604 (mp10) cc_final: 0.8331 (mm-40) REVERT: A 266 GLU cc_start: 0.7437 (pp20) cc_final: 0.7226 (pp20) REVERT: A 267 PHE cc_start: 0.8256 (p90) cc_final: 0.7504 (p90) REVERT: A 274 GLU cc_start: 0.6560 (pm20) cc_final: 0.6105 (pm20) REVERT: A 276 PHE cc_start: 0.8020 (p90) cc_final: 0.7806 (p90) REVERT: A 292 PHE cc_start: 0.7740 (t80) cc_final: 0.7139 (t80) REVERT: A 338 ASP cc_start: 0.6818 (m-30) cc_final: 0.6562 (m-30) REVERT: B 74 MET cc_start: -0.0428 (mmp) cc_final: -0.1414 (mmp) REVERT: B 114 MET cc_start: 0.7590 (mmm) cc_final: 0.7179 (mmm) REVERT: B 122 LYS cc_start: 0.8045 (tmtt) cc_final: 0.7629 (tmtt) REVERT: B 127 MET cc_start: 0.7104 (mmp) cc_final: 0.6891 (mmp) REVERT: B 214 ARG cc_start: 0.7647 (ttp80) cc_final: 0.6977 (ttp80) REVERT: B 260 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: B 339 LYS cc_start: 0.8382 (mptt) cc_final: 0.8157 (mptt) REVERT: B 365 MET cc_start: 0.4826 (ppp) cc_final: 0.4276 (ppp) REVERT: C 74 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8123 (mtp180) REVERT: C 79 TRP cc_start: 0.8709 (m100) cc_final: 0.8470 (m100) REVERT: C 102 VAL cc_start: 0.8066 (p) cc_final: 0.7745 (t) REVERT: C 195 MET cc_start: 0.7699 (mmm) cc_final: 0.7202 (mmm) REVERT: C 326 LYS cc_start: 0.8378 (mmmt) cc_final: 0.8074 (mmmt) REVERT: D 5 GLU cc_start: 0.6847 (pm20) cc_final: 0.6518 (pm20) REVERT: D 65 LYS cc_start: 0.7878 (mttp) cc_final: 0.7618 (mttp) REVERT: D 74 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6655 (tm-30) REVERT: D 106 LYS cc_start: 0.8298 (mppt) cc_final: 0.8020 (mppt) REVERT: D 126 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6794 (mm-30) REVERT: D 155 GLU cc_start: 0.6963 (tt0) cc_final: 0.6736 (tt0) REVERT: D 166 SER cc_start: 0.8071 (m) cc_final: 0.7745 (t) REVERT: D 186 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7779 (ttmm) REVERT: D 204 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6900 (mm-30) REVERT: E 14 LYS cc_start: 0.7776 (mptt) cc_final: 0.7514 (mptt) REVERT: E 80 LYS cc_start: 0.7587 (mttp) cc_final: 0.7130 (mttp) REVERT: E 88 LYS cc_start: 0.8245 (tmmt) cc_final: 0.7909 (tmmt) REVERT: E 129 MET cc_start: 0.7147 (ttm) cc_final: 0.6923 (ttm) REVERT: F 39 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6802 (mm-30) REVERT: F 70 VAL cc_start: 0.8444 (p) cc_final: 0.8225 (t) REVERT: F 110 GLU cc_start: 0.7232 (mp0) cc_final: 0.6920 (mp0) REVERT: F 141 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6359 (mm-30) REVERT: F 163 GLU cc_start: 0.6987 (tp30) cc_final: 0.6445 (tp30) REVERT: F 167 ASN cc_start: 0.7429 (m110) cc_final: 0.7139 (m-40) REVERT: G 51 MET cc_start: 0.7021 (tpp) cc_final: 0.6782 (mpp) outliers start: 37 outliers final: 29 residues processed: 480 average time/residue: 0.3631 time to fit residues: 233.2022 Evaluate side-chains 495 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 464 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain H residue 213 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 0.0970 chunk 71 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS D 140 ASN D 278 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 15373 Z= 0.444 Angle : 0.609 11.737 20807 Z= 0.316 Chirality : 0.048 0.163 2281 Planarity : 0.004 0.053 2674 Dihedral : 6.377 89.375 2114 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.21 % Allowed : 17.82 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.54 (0.20), residues: 1863 helix: 1.33 (0.20), residues: 687 sheet: -0.32 (0.27), residues: 357 loop : -0.03 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 224 HIS 0.008 0.001 HIS F 137 PHE 0.035 0.002 PHE B 340 TYR 0.054 0.002 TYR E 74 ARG 0.009 0.001 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 479 time to evaluate : 1.784 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7161 (mtm-85) cc_final: 0.6846 (mtm-85) REVERT: A 128 GLU cc_start: 0.7586 (tt0) cc_final: 0.7265 (tt0) REVERT: A 229 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6909 (mm-30) REVERT: A 237 ASP cc_start: 0.6711 (t70) cc_final: 0.6290 (t0) REVERT: A 240 LYS cc_start: 0.8302 (mttp) cc_final: 0.7767 (mttp) REVERT: A 266 GLU cc_start: 0.7452 (pp20) cc_final: 0.7240 (pp20) REVERT: A 267 PHE cc_start: 0.8322 (p90) cc_final: 0.7523 (p90) REVERT: A 274 GLU cc_start: 0.6721 (pm20) cc_final: 0.6228 (pm20) REVERT: A 292 PHE cc_start: 0.7829 (t80) cc_final: 0.7210 (t80) REVERT: A 333 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7303 (ttp80) REVERT: A 338 ASP cc_start: 0.6843 (m-30) cc_final: 0.6581 (m-30) REVERT: B 74 MET cc_start: -0.0341 (mmp) cc_final: -0.1305 (mmp) REVERT: B 114 MET cc_start: 0.7644 (mmm) cc_final: 0.7238 (mmm) REVERT: B 122 LYS cc_start: 0.8118 (tmtt) cc_final: 0.7682 (tmtt) REVERT: B 127 MET cc_start: 0.7237 (mmp) cc_final: 0.7016 (mmp) REVERT: B 214 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7032 (ttp80) REVERT: B 260 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6529 (mp0) REVERT: B 339 LYS cc_start: 0.8381 (mptt) cc_final: 0.8143 (mptt) REVERT: B 346 ASP cc_start: 0.6910 (p0) cc_final: 0.6286 (p0) REVERT: B 365 MET cc_start: 0.4909 (ppp) cc_final: 0.4361 (ppp) REVERT: C 74 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7841 (mtp180) REVERT: C 102 VAL cc_start: 0.8023 (p) cc_final: 0.7744 (t) REVERT: C 195 MET cc_start: 0.7739 (mmm) cc_final: 0.7164 (mmm) REVERT: C 326 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8106 (mmmt) REVERT: D 5 GLU cc_start: 0.6864 (pm20) cc_final: 0.6524 (pm20) REVERT: D 65 LYS cc_start: 0.7865 (mttp) cc_final: 0.7599 (mttp) REVERT: D 74 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6661 (tm-30) REVERT: D 106 LYS cc_start: 0.8301 (mppt) cc_final: 0.7997 (mppt) REVERT: D 126 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6857 (mm-30) REVERT: D 166 SER cc_start: 0.8056 (m) cc_final: 0.7802 (t) REVERT: D 186 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7770 (ttmm) REVERT: D 204 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6982 (mm-30) REVERT: E 14 LYS cc_start: 0.7769 (mptt) cc_final: 0.7533 (mptt) REVERT: E 88 LYS cc_start: 0.8211 (tmmt) cc_final: 0.7877 (tmmt) REVERT: F 39 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6816 (mm-30) REVERT: F 95 MET cc_start: 0.8200 (mtp) cc_final: 0.7993 (mtm) REVERT: F 110 GLU cc_start: 0.7244 (mp0) cc_final: 0.6944 (mp0) REVERT: F 139 MET cc_start: 0.8442 (mtt) cc_final: 0.8020 (mtp) REVERT: F 141 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6305 (mm-30) REVERT: F 163 GLU cc_start: 0.7035 (tp30) cc_final: 0.6393 (tp30) REVERT: G 51 MET cc_start: 0.7036 (tpp) cc_final: 0.6790 (mpp) outliers start: 36 outliers final: 29 residues processed: 489 average time/residue: 0.3601 time to fit residues: 236.4078 Evaluate side-chains 506 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 475 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 168 optimal weight: 3.9990 chunk 145 optimal weight: 0.0010 chunk 15 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 278 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15373 Z= 0.191 Angle : 0.540 11.323 20807 Z= 0.281 Chirality : 0.044 0.160 2281 Planarity : 0.004 0.048 2674 Dihedral : 5.991 88.178 2110 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.60 % Allowed : 18.56 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.64 (0.20), residues: 1863 helix: 1.44 (0.20), residues: 689 sheet: -0.21 (0.28), residues: 348 loop : -0.05 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 160 HIS 0.003 0.001 HIS F 137 PHE 0.022 0.001 PHE A 276 TYR 0.053 0.002 TYR E 74 ARG 0.008 0.001 ARG D 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 470 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6812 (mtm-85) REVERT: A 128 GLU cc_start: 0.7575 (tt0) cc_final: 0.7252 (tt0) REVERT: A 237 ASP cc_start: 0.6457 (t70) cc_final: 0.6038 (t0) REVERT: A 266 GLU cc_start: 0.7413 (pp20) cc_final: 0.7205 (pp20) REVERT: A 267 PHE cc_start: 0.8278 (p90) cc_final: 0.7439 (p90) REVERT: A 274 GLU cc_start: 0.6490 (pm20) cc_final: 0.5989 (pm20) REVERT: A 292 PHE cc_start: 0.7792 (t80) cc_final: 0.7198 (t80) REVERT: A 333 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7198 (ttp80) REVERT: A 338 ASP cc_start: 0.6755 (m-30) cc_final: 0.6493 (m-30) REVERT: B 74 MET cc_start: -0.0350 (mmp) cc_final: -0.1351 (mmp) REVERT: B 114 MET cc_start: 0.7466 (mmm) cc_final: 0.7101 (mmm) REVERT: B 122 LYS cc_start: 0.8091 (tmtt) cc_final: 0.7638 (tmtt) REVERT: B 127 MET cc_start: 0.7166 (mmp) cc_final: 0.6946 (mmp) REVERT: B 260 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: B 339 LYS cc_start: 0.8334 (mptt) cc_final: 0.8131 (mptt) REVERT: B 365 MET cc_start: 0.4819 (ppp) cc_final: 0.4333 (ppp) REVERT: C 70 CYS cc_start: 0.7489 (p) cc_final: 0.7146 (p) REVERT: C 74 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8127 (mtp180) REVERT: C 102 VAL cc_start: 0.8026 (p) cc_final: 0.7372 (t) REVERT: C 108 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6821 (mt-10) REVERT: C 195 MET cc_start: 0.7699 (mmm) cc_final: 0.7212 (mmm) REVERT: C 326 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8124 (mmmt) REVERT: D 5 GLU cc_start: 0.6782 (pm20) cc_final: 0.6492 (pm20) REVERT: D 65 LYS cc_start: 0.7858 (mttp) cc_final: 0.7595 (mttp) REVERT: D 74 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6615 (tm-30) REVERT: D 106 LYS cc_start: 0.8287 (mppt) cc_final: 0.8026 (mppt) REVERT: D 126 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6774 (mm-30) REVERT: D 155 GLU cc_start: 0.6961 (tt0) cc_final: 0.6710 (tt0) REVERT: D 166 SER cc_start: 0.8084 (m) cc_final: 0.7790 (t) REVERT: D 186 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7734 (ttmm) REVERT: D 204 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6913 (mm-30) REVERT: E 14 LYS cc_start: 0.7781 (mptt) cc_final: 0.7492 (mptt) REVERT: E 80 LYS cc_start: 0.7499 (mttp) cc_final: 0.7069 (mttp) REVERT: E 88 LYS cc_start: 0.8189 (tmmt) cc_final: 0.7844 (tmmt) REVERT: F 39 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6724 (mm-30) REVERT: F 110 GLU cc_start: 0.7198 (mp0) cc_final: 0.6885 (mp0) REVERT: F 139 MET cc_start: 0.8416 (mtt) cc_final: 0.7944 (mtp) REVERT: F 141 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6206 (mm-30) REVERT: F 163 GLU cc_start: 0.7010 (tp30) cc_final: 0.6400 (tp30) REVERT: G 51 MET cc_start: 0.6966 (tpp) cc_final: 0.6725 (mpp) REVERT: H 200 MET cc_start: 0.7498 (mmm) cc_final: 0.7298 (mmm) outliers start: 26 outliers final: 21 residues processed: 476 average time/residue: 0.3624 time to fit residues: 230.9682 Evaluate side-chains 489 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 466 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 128 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118919 restraints weight = 21681.908| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.09 r_work: 0.3327 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15373 Z= 0.224 Angle : 0.545 11.239 20807 Z= 0.283 Chirality : 0.044 0.169 2281 Planarity : 0.004 0.048 2674 Dihedral : 5.950 88.717 2110 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.60 % Allowed : 18.87 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.64 (0.20), residues: 1863 helix: 1.48 (0.20), residues: 687 sheet: -0.25 (0.28), residues: 352 loop : -0.06 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 185 HIS 0.004 0.001 HIS F 137 PHE 0.045 0.002 PHE B 340 TYR 0.052 0.002 TYR E 74 ARG 0.009 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4849.37 seconds wall clock time: 86 minutes 50.60 seconds (5210.60 seconds total)