Starting phenix.real_space_refine on Tue Dec 12 10:19:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/12_2023/7sh2_25122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/12_2023/7sh2_25122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/12_2023/7sh2_25122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/12_2023/7sh2_25122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/12_2023/7sh2_25122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/12_2023/7sh2_25122_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 36 5.49 5 Mg 4 5.21 5 S 113 5.16 5 C 13174 2.51 5 N 3597 2.21 5 O 4009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20933 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3309 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2489 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2569 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2617 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2692 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2178 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 6 Chain: "G" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2313 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 4, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2145 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 5 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.24, per 1000 atoms: 0.49 Number of scatterers: 20933 At special positions: 0 Unit cell: (135.792, 125.856, 142.416, 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 113 16.00 P 36 15.00 Mg 4 11.99 O 4009 8.00 N 3597 7.00 C 13174 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: 8.42 Conformation dependent library (CDL) restraints added in 3.3 seconds 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 18 sheets defined 44.4% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 116 through 129 Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.529A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 386 removed outlier: 5.505A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.526A pdb=" N MET A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 433 removed outlier: 4.677A pdb=" N LYS A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 470 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 69 through 72 removed outlier: 4.229A pdb=" N ALA B 72 " --> pdb=" O ARG B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 88 through 97 Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 259 removed outlier: 4.234A pdb=" N LYS B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 321 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 75 through 78 No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.508A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 257 through 269 Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.813A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 312 Processing helix chain 'C' and resid 316 through 331 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 44 through 53 Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.730A pdb=" N MET D 88 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS D 89 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 90 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 91 " --> pdb=" O MET D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 91' Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 194 through 207 removed outlier: 5.294A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.585A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 35 removed outlier: 4.200A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 150 through 160 removed outlier: 3.776A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 3.831A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'F' and resid 13 through 29 Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.506A pdb=" N SER F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 219 Processing helix chain 'F' and resid 240 through 255 Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'G' and resid 18 through 27 removed outlier: 3.813A pdb=" N CYS G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 32 No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 86 through 95 removed outlier: 4.261A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 160 through 173 removed outlier: 4.298A pdb=" N GLU G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 248 removed outlier: 4.164A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 328 Processing helix chain 'H' and resid 11 through 26 removed outlier: 3.997A pdb=" N ASN H 14 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 98 through 102 Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 235 through 242 Processing helix chain 'H' and resid 327 through 338 removed outlier: 3.929A pdb=" N ILE H 335 " --> pdb=" O ASN H 331 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Proline residue: H 337 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 260 through 262 removed outlier: 7.696A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 148 through 150 removed outlier: 7.785A pdb=" N LEU A 183 " --> pdb=" O THR A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.021A pdb=" N SER B 48 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 162 through 166 removed outlier: 9.291A pdb=" N LEU C 49 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE C 143 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE C 51 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 145 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLY C 53 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 147 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU C 80 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 185 through 189 removed outlier: 3.753A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 186 through 190 removed outlier: 3.500A pdb=" N LEU E 39 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 96 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 95 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 73 through 78 removed outlier: 4.085A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 42 through 44 removed outlier: 4.047A pdb=" N THR F 43 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 121 through 123 removed outlier: 3.573A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY F 157 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS F 203 " --> pdb=" O PHE F 160 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 263 through 266 Processing sheet with id= K, first strand: chain 'F' and resid 442 through 445 removed outlier: 3.522A pdb=" N ASP F 445 " --> pdb=" O GLY F 462 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 11 through 15 Processing sheet with id= M, first strand: chain 'G' and resid 37 through 41 removed outlier: 3.585A pdb=" N LEU G 82 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE G 41 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET G 80 " --> pdb=" O ILE G 41 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 45 through 52 removed outlier: 3.885A pdb=" N ASN G 52 " --> pdb=" O ILE G 56 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET G 259 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.113A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA G 193 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE G 205 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.648A pdb=" N THR H 6 " --> pdb=" O ILE H 118 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE H 118 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU H 139 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE H 116 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL H 137 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE H 118 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE H 135 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 91 through 97 removed outlier: 3.523A pdb=" N GLU H 375 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN H 363 " --> pdb=" O ILE H 349 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 322 through 324 removed outlier: 4.659A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 254 " --> pdb=" O ILE H 322 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE H 324 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL H 252 " --> pdb=" O PHE H 324 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR H 264 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU H 255 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET H 284 " --> pdb=" O ALA H 265 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2454 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.41 Time building geometry restraints manager: 9.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6866 1.36 - 1.51: 5506 1.51 - 1.66: 8790 1.66 - 1.80: 100 1.80 - 1.95: 70 Bond restraints: 21332 Sorted by residual: bond pdb=" N MET F 224 " pdb=" CA MET F 224 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.42e+00 bond pdb=" CG1 ILE G 324 " pdb=" CD1 ILE G 324 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.36e+00 bond pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" C THR G 29 " pdb=" N PRO G 30 " ideal model delta sigma weight residual 1.335 1.349 -0.015 1.28e-02 6.10e+03 1.32e+00 bond pdb=" CA ASN F 286 " pdb=" CB ASN F 286 " ideal model delta sigma weight residual 1.535 1.557 -0.021 1.90e-02 2.77e+03 1.27e+00 ... (remaining 21327 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.96: 657 106.96 - 114.26: 12826 114.26 - 121.55: 10546 121.55 - 128.84: 4752 128.84 - 136.14: 138 Bond angle restraints: 28919 Sorted by residual: angle pdb=" C SER E 79 " pdb=" CA SER E 79 " pdb=" CB SER E 79 " ideal model delta sigma weight residual 116.54 110.32 6.22 1.15e+00 7.56e-01 2.93e+01 angle pdb=" CA PRO F 48 " pdb=" N PRO F 48 " pdb=" CD PRO F 48 " ideal model delta sigma weight residual 112.00 105.04 6.96 1.40e+00 5.10e-01 2.47e+01 angle pdb=" C ILE G 324 " pdb=" N GLU G 325 " pdb=" CA GLU G 325 " ideal model delta sigma weight residual 120.29 114.08 6.21 1.42e+00 4.96e-01 1.92e+01 angle pdb=" N GLU G 325 " pdb=" CA GLU G 325 " pdb=" CB GLU G 325 " ideal model delta sigma weight residual 110.16 116.34 -6.18 1.48e+00 4.57e-01 1.74e+01 angle pdb=" N VAL G 16 " pdb=" CA VAL G 16 " pdb=" C VAL G 16 " ideal model delta sigma weight residual 113.53 109.51 4.02 9.80e-01 1.04e+00 1.68e+01 ... (remaining 28914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 12648 35.05 - 70.11: 327 70.11 - 105.16: 21 105.16 - 140.22: 2 140.22 - 175.27: 1 Dihedral angle restraints: 12999 sinusoidal: 5537 harmonic: 7462 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 177.99 122.01 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 57.22 -124.95 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C4' DA T 22 " pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " pdb=" P DG T 23 " ideal model delta sinusoidal sigma weight residual -140.00 35.27 -175.27 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 12996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2543 0.043 - 0.085: 593 0.085 - 0.128: 193 0.128 - 0.170: 11 0.170 - 0.213: 6 Chirality restraints: 3346 Sorted by residual: chirality pdb=" CB ILE G 103 " pdb=" CA ILE G 103 " pdb=" CG1 ILE G 103 " pdb=" CG2 ILE G 103 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE G 251 " pdb=" CA ILE G 251 " pdb=" CG1 ILE G 251 " pdb=" CG2 ILE G 251 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA THR F 47 " pdb=" N THR F 47 " pdb=" C THR F 47 " pdb=" CB THR F 47 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 3343 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " -0.085 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO F 48 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 167 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO C 168 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 488 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 489 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.025 5.00e-02 4.00e+02 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 395 2.69 - 3.24: 19941 3.24 - 3.79: 33232 3.79 - 4.35: 42987 4.35 - 4.90: 71254 Nonbonded interactions: 167809 Sorted by model distance: nonbonded pdb=" O1B AGS B 401 " pdb="MG MG B 402 " model vdw 2.135 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.144 2.170 nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.169 2.170 nonbonded pdb=" O LEU G 326 " pdb=" OG1 THR G 330 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR F 92 " pdb=" OG1 THR F 218 " model vdw 2.202 2.440 ... (remaining 167804 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.210 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 55.310 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 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 : 0.002 0.060 21332 Z= 0.143 Angle : 0.560 9.916 28919 Z= 0.292 Chirality : 0.041 0.213 3346 Planarity : 0.004 0.124 3560 Dihedral : 15.294 175.269 8131 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2497 helix: 1.46 (0.15), residues: 1225 sheet: 0.27 (0.27), residues: 440 loop : -1.43 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 259 HIS 0.004 0.001 HIS F 74 PHE 0.023 0.001 PHE F 205 TYR 0.015 0.001 TYR E 324 ARG 0.006 0.000 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 2.364 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.2844 time to fit residues: 135.7363 Evaluate side-chains 207 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 5.9990 chunk 191 optimal weight: 0.0040 chunk 106 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 229 optimal weight: 20.0000 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN D 124 HIS D 236 GLN D 305 HIS D 313 ASN E 93 HIS F 463 GLN G 9 ASN G 54 HIS G 190 ASN H 37 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21332 Z= 0.156 Angle : 0.503 8.399 28919 Z= 0.257 Chirality : 0.040 0.165 3346 Planarity : 0.003 0.045 3560 Dihedral : 11.750 175.192 3056 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.96 % Allowed : 7.62 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2497 helix: 1.65 (0.15), residues: 1226 sheet: 0.20 (0.26), residues: 448 loop : -1.32 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 259 HIS 0.005 0.001 HIS G 54 PHE 0.014 0.001 PHE F 242 TYR 0.017 0.001 TYR F 233 ARG 0.004 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 244 time to evaluate : 2.577 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 258 average time/residue: 0.3189 time to fit residues: 132.0112 Evaluate side-chains 231 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 2.297 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1956 time to fit residues: 9.0089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 204 optimal weight: 0.0870 chunk 228 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 184 optimal weight: 0.0570 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 64 HIS C 213 GLN D 124 HIS D 196 ASN E 164 ASN G 54 HIS G 190 ASN H 37 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21332 Z= 0.168 Angle : 0.498 8.673 28919 Z= 0.254 Chirality : 0.040 0.169 3346 Planarity : 0.003 0.043 3560 Dihedral : 11.589 175.075 3056 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.70 % Allowed : 10.75 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.66 (0.18), residues: 2497 helix: 1.65 (0.15), residues: 1224 sheet: 0.24 (0.26), residues: 438 loop : -1.29 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 415 HIS 0.005 0.001 HIS B 64 PHE 0.016 0.001 PHE E 328 TYR 0.020 0.001 TYR B 71 ARG 0.005 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 242 time to evaluate : 2.336 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 250 average time/residue: 0.3429 time to fit residues: 135.3343 Evaluate side-chains 225 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 2.371 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2085 time to fit residues: 6.4380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 119 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 218 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 213 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS E 164 ASN F 226 ASN H 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21332 Z= 0.166 Angle : 0.496 9.668 28919 Z= 0.253 Chirality : 0.040 0.163 3346 Planarity : 0.003 0.051 3560 Dihedral : 11.517 175.116 3056 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.00 % Allowed : 12.45 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2497 helix: 1.63 (0.15), residues: 1224 sheet: 0.15 (0.26), residues: 439 loop : -1.31 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 259 HIS 0.004 0.001 HIS B 64 PHE 0.015 0.001 PHE G 202 TYR 0.031 0.001 TYR B 71 ARG 0.007 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 2.381 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 255 average time/residue: 0.3324 time to fit residues: 133.1022 Evaluate side-chains 228 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 219 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1925 time to fit residues: 6.6782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 213 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS E 164 ASN F 67 GLN G 54 HIS H 37 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21332 Z= 0.221 Angle : 0.547 9.130 28919 Z= 0.278 Chirality : 0.041 0.175 3346 Planarity : 0.004 0.055 3560 Dihedral : 11.640 175.879 3056 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.22 % Allowed : 14.06 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2497 helix: 1.41 (0.15), residues: 1224 sheet: 0.08 (0.26), residues: 437 loop : -1.42 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 415 HIS 0.006 0.001 HIS D 124 PHE 0.017 0.002 PHE E 328 TYR 0.027 0.002 TYR B 71 ARG 0.008 0.001 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 2.537 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 261 average time/residue: 0.3253 time to fit residues: 136.0732 Evaluate side-chains 230 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 2.337 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2085 time to fit residues: 8.1242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 4.9990 chunk 220 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 244 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 236 GLN G 262 HIS H 37 ASN H 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21332 Z= 0.189 Angle : 0.519 9.649 28919 Z= 0.265 Chirality : 0.041 0.289 3346 Planarity : 0.003 0.044 3560 Dihedral : 11.553 175.365 3056 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.74 % Allowed : 15.27 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2497 helix: 1.36 (0.15), residues: 1227 sheet: 0.08 (0.26), residues: 437 loop : -1.37 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 259 HIS 0.005 0.001 HIS H 100 PHE 0.018 0.001 PHE F 249 TYR 0.024 0.001 TYR B 71 ARG 0.007 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 2.558 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 239 average time/residue: 0.3370 time to fit residues: 128.7752 Evaluate side-chains 209 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 2.436 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2001 time to fit residues: 7.1186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 136 optimal weight: 0.0170 chunk 243 optimal weight: 20.0000 chunk 152 optimal weight: 0.0050 chunk 148 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.5434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN C 213 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 HIS H 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21332 Z= 0.154 Angle : 0.511 9.561 28919 Z= 0.258 Chirality : 0.040 0.198 3346 Planarity : 0.003 0.044 3560 Dihedral : 11.435 175.130 3056 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.83 % Allowed : 15.97 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2497 helix: 1.50 (0.15), residues: 1226 sheet: 0.09 (0.26), residues: 437 loop : -1.34 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 415 HIS 0.005 0.001 HIS G 54 PHE 0.020 0.001 PHE F 249 TYR 0.020 0.001 TYR A 339 ARG 0.010 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 212 time to evaluate : 2.331 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 226 average time/residue: 0.3201 time to fit residues: 116.9631 Evaluate side-chains 209 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 2.368 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1970 time to fit residues: 7.4584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 166 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 191 optimal weight: 0.0570 chunk 221 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN B 41 ASN C 213 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN H 245 ASN H 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21332 Z= 0.163 Angle : 0.523 14.180 28919 Z= 0.263 Chirality : 0.040 0.371 3346 Planarity : 0.003 0.043 3560 Dihedral : 11.402 175.254 3056 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.48 % Allowed : 16.36 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2497 helix: 1.48 (0.15), residues: 1227 sheet: 0.08 (0.26), residues: 439 loop : -1.34 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 296 HIS 0.006 0.001 HIS F 263 PHE 0.017 0.001 PHE G 202 TYR 0.017 0.001 TYR E 92 ARG 0.007 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 2.378 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 217 average time/residue: 0.3211 time to fit residues: 112.9377 Evaluate side-chains 199 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 193 time to evaluate : 2.591 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1957 time to fit residues: 5.8290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN C 333 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21332 Z= 0.243 Angle : 0.588 13.089 28919 Z= 0.295 Chirality : 0.042 0.375 3346 Planarity : 0.004 0.047 3560 Dihedral : 11.593 176.350 3056 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.48 % Allowed : 16.49 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.17), residues: 2497 helix: 1.16 (0.15), residues: 1225 sheet: -0.11 (0.26), residues: 449 loop : -1.39 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 415 HIS 0.005 0.001 HIS F 263 PHE 0.022 0.002 PHE F 246 TYR 0.021 0.002 TYR B 163 ARG 0.011 0.001 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 224 time to evaluate : 2.497 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 231 average time/residue: 0.3573 time to fit residues: 126.6937 Evaluate side-chains 206 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2187 time to fit residues: 6.0638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 0.0670 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 155 optimal weight: 0.4980 chunk 123 optimal weight: 0.0970 chunk 159 optimal weight: 2.9990 overall best weight: 0.9118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS H 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 21332 Z= 0.204 Angle : 0.559 14.307 28919 Z= 0.282 Chirality : 0.042 0.392 3346 Planarity : 0.003 0.044 3560 Dihedral : 11.509 175.677 3056 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.13 % Allowed : 16.67 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.17), residues: 2497 helix: 1.21 (0.15), residues: 1226 sheet: -0.08 (0.26), residues: 445 loop : -1.40 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 259 HIS 0.006 0.001 HIS F 263 PHE 0.016 0.001 PHE G 40 TYR 0.019 0.001 TYR E 92 ARG 0.013 0.001 ARG F 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 2.388 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 210 average time/residue: 0.3378 time to fit residues: 112.6697 Evaluate side-chains 201 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 2.449 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1907 time to fit residues: 4.5144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 185 optimal weight: 0.0170 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 201 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 54 HIS H 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.184844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.150553 restraints weight = 29087.967| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.16 r_work: 0.3863 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21332 Z= 0.174 Angle : 0.549 14.485 28919 Z= 0.274 Chirality : 0.041 0.377 3346 Planarity : 0.003 0.044 3560 Dihedral : 11.406 175.453 3056 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.26 % Allowed : 16.75 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2497 helix: 1.32 (0.15), residues: 1226 sheet: -0.03 (0.26), residues: 444 loop : -1.40 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 259 HIS 0.005 0.001 HIS G 54 PHE 0.018 0.001 PHE A 456 TYR 0.028 0.001 TYR A 339 ARG 0.010 0.000 ARG F 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4378.18 seconds wall clock time: 80 minutes 50.86 seconds (4850.86 seconds total)