Starting phenix.real_space_refine on Sat Nov 18 02:33:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2023/8fs3_29412_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2023/8fs3_29412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2023/8fs3_29412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2023/8fs3_29412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2023/8fs3_29412_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs3_29412/11_2023/8fs3_29412_updated.pdb" } resolution = 2.93 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= 0.032 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 40 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 13358 2.51 5 N 3643 2.21 5 O 4063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F ARG 461": "NH1" <-> "NH2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 314": "OE1" <-> "OE2" Residue "G GLU 329": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21222 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3564 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 419} Chain breaks: 2 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: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2593 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2240 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 7 Chain: "G" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2257 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 4, 'TRANS': 280} Chain breaks: 3 Chain: "H" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2017 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 6 Chain: "I" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 344 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} 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: 10.93, per 1000 atoms: 0.52 Number of scatterers: 21222 At special positions: 0 Unit cell: (111.78, 134.964, 137.448, 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 114 16.00 P 40 15.00 Mg 4 11.99 O 4063 8.00 N 3643 7.00 C 13358 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: 8.78 Conformation dependent library (CDL) restraints added in 3.6 seconds 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 16 sheets defined 46.1% alpha, 14.5% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 8.89 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 removed outlier: 3.665A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 No H-bonds generated for 'chain 'A' and resid 127 through 130' Processing helix chain 'A' and resid 162 through 173 removed outlier: 4.444A pdb=" N PHE A 166 " --> pdb=" O MET A 163 " (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 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 374 through 386 removed outlier: 5.127A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.590A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.570A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 469 removed outlier: 3.890A pdb=" N TYR A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 487 through 497 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 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 71 removed outlier: 8.081A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 152 through 157 removed outlier: 4.151A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) 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 216 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 256 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 282 through 300 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' 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 43 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.529A pdb=" N MET C 78 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.872A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 136 removed outlier: 4.282A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 252 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.011A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.922A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 316 through 335 removed outlier: 4.202A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) 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 43 through 54 removed outlier: 3.775A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 91 Proline residue: D 85 - end of helix removed outlier: 4.433A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.840A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) 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 removed outlier: 4.497A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 194 through 207 removed outlier: 5.249A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.553A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 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 21 through 31 Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 103 through 118 removed outlier: 4.098A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE E 107 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU E 112 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 113 " --> pdb=" O GLN E 110 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 114 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E 115 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA E 117 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN E 118 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 150 through 160 removed outlier: 4.099A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 209 Processing helix chain 'E' and resid 216 through 226 removed outlier: 4.098A pdb=" N ARG E 221 " --> pdb=" O ILE E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 242 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 Processing helix chain 'E' and resid 296 through 309 removed outlier: 3.845A pdb=" N ASP E 309 " --> pdb=" O PHE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 338 through 353 Processing helix chain 'F' and resid 13 through 29 Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 97 through 111 Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 241 through 255 removed outlier: 4.550A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL F 253 " --> pdb=" O PHE F 249 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG F 255 " --> pdb=" O ARG F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 86 through 92 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 251 removed outlier: 3.927A pdb=" N LYS G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE G 251 " --> pdb=" O LYS G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 329 Processing helix chain 'H' and resid 10 through 26 Processing helix chain 'H' and resid 98 through 102 Processing helix chain 'H' and resid 234 through 243 Processing helix chain 'H' and resid 327 through 338 removed outlier: 3.902A 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 264 removed outlier: 6.673A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A 219 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU A 107 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE A 221 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N GLY A 109 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A 223 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 163 removed outlier: 3.591A pdb=" N GLY B 49 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 6.384A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 6.291A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 189 removed outlier: 6.514A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 4 through 7 Processing sheet with id= G, first strand: chain 'F' and resid 34 through 38 removed outlier: 3.552A pdb=" N ARG F 41 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 462 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 93 through 95 removed outlier: 3.720A pdb=" N GLU F 94 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 408 through 411 removed outlier: 3.996A pdb=" N VAL F 267 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU F 280 " --> pdb=" O VAL F 267 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 11 through 15 removed outlier: 3.641A pdb=" N PHE G 121 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.212A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE G 304 " --> pdb=" O SER G 271 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU G 270 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 233 through 238 removed outlier: 3.548A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.632A pdb=" N PHE H 3 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE H 116 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU H 139 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE H 116 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL H 137 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE H 118 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE H 135 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 92 through 97 removed outlier: 7.021A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE H 40 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS H 52 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 348 through 353 Processing sheet with id= P, first strand: chain 'H' and resid 321 through 324 removed outlier: 3.590A pdb=" N GLU H 251 " --> pdb=" O PHE H 266 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 7.57 Time building geometry restraints manager: 9.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6925 1.36 - 1.50: 5618 1.50 - 1.65: 8916 1.65 - 1.80: 81 1.80 - 1.95: 89 Bond restraints: 21629 Sorted by residual: bond pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" C LYS A 498 " pdb=" O LYS A 498 " ideal model delta sigma weight residual 1.236 1.277 -0.041 1.28e-02 6.10e+03 1.03e+01 bond pdb=" N ILE H 360 " pdb=" CA ILE H 360 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.00e+01 bond pdb=" N ILE F 432 " pdb=" CA ILE F 432 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.47e+00 bond pdb=" N TRP H 352 " pdb=" CA TRP H 352 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.21e-02 6.83e+03 8.41e+00 ... (remaining 21624 not shown) Histogram of bond angle deviations from ideal: 96.10 - 104.12: 334 104.12 - 112.13: 11272 112.13 - 120.15: 8602 120.15 - 128.16: 8965 128.16 - 136.18: 161 Bond angle restraints: 29334 Sorted by residual: angle pdb=" N GLU C 294 " pdb=" CA GLU C 294 " pdb=" C GLU C 294 " ideal model delta sigma weight residual 112.89 107.10 5.79 1.24e+00 6.50e-01 2.18e+01 angle pdb=" C PRO D 133 " pdb=" CA PRO D 133 " pdb=" CB PRO D 133 " ideal model delta sigma weight residual 112.89 107.58 5.31 1.31e+00 5.83e-01 1.64e+01 angle pdb=" C TYR A 497 " pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 122.73 116.23 6.50 1.61e+00 3.86e-01 1.63e+01 angle pdb=" N GLN A 283 " pdb=" CA GLN A 283 " pdb=" C GLN A 283 " ideal model delta sigma weight residual 113.17 108.18 4.99 1.26e+00 6.30e-01 1.57e+01 angle pdb=" N GLU B 182 " pdb=" CA GLU B 182 " pdb=" C GLU B 182 " ideal model delta sigma weight residual 113.72 108.86 4.86 1.30e+00 5.92e-01 1.40e+01 ... (remaining 29329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 12424 34.54 - 69.08: 652 69.08 - 103.62: 26 103.62 - 138.16: 2 138.16 - 172.69: 1 Dihedral angle restraints: 13105 sinusoidal: 5564 harmonic: 7541 Sorted by residual: dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 127.31 172.69 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 74.45 -134.45 1 2.00e+01 2.50e-03 4.08e+01 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 -60.00 56.94 -116.95 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 13102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2983 0.068 - 0.136: 394 0.136 - 0.204: 23 0.204 - 0.272: 2 0.272 - 0.340: 1 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CB THR D 47 " pdb=" CA THR D 47 " pdb=" OG1 THR D 47 " pdb=" CG2 THR D 47 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE B 47 " pdb=" CA ILE B 47 " pdb=" CG1 ILE B 47 " pdb=" CG2 ILE B 47 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3400 not shown) Planarity restraints: 3593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 213 " 0.026 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE F 213 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE F 213 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE F 213 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE F 213 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 213 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 213 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 294 " 0.020 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP A 294 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 294 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 294 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 294 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 294 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 294 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 294 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 294 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 294 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 180 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LYS B 180 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS B 180 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 181 " -0.019 2.00e-02 2.50e+03 ... (remaining 3590 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 156 2.51 - 3.11: 15397 3.11 - 3.70: 33314 3.70 - 4.30: 48749 4.30 - 4.90: 81231 Nonbonded interactions: 178847 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O3A AGS A 602 " model vdw 1.912 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G AGS C 402 " model vdw 1.943 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 1.965 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 1.966 2.170 nonbonded pdb=" OG SER A 116 " pdb="MG MG A 601 " model vdw 1.983 2.170 ... (remaining 178842 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: 5.100 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: 20.270 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 62.050 Find NCS groups from input model: 0.840 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 0.054 21629 Z= 0.262 Angle : 0.675 10.904 29334 Z= 0.397 Chirality : 0.045 0.340 3403 Planarity : 0.005 0.095 3593 Dihedral : 18.366 172.694 8185 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.30 % Allowed : 27.80 % Favored : 67.90 % 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: 0.21 (0.17), residues: 2518 helix: 0.91 (0.15), residues: 1238 sheet: -0.12 (0.24), residues: 516 loop : -0.76 (0.23), residues: 764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 280 time to evaluate : 2.705 Fit side-chains revert: symmetry clash outliers start: 100 outliers final: 78 residues processed: 363 average time/residue: 1.0660 time to fit residues: 452.9431 Evaluate side-chains 337 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 259 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 71 residues processed: 8 average time/residue: 0.4146 time to fit residues: 7.0811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 77 optimal weight: 0.0000 chunk 121 optimal weight: 0.0770 chunk 148 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 overall best weight: 1.0946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 284 ASN B 102 HIS C 298 HIS D 24 GLN D 207 GLN D 311 ASN E 104 ASN F 291 HIS H 355 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21629 Z= 0.240 Angle : 0.574 10.550 29334 Z= 0.297 Chirality : 0.043 0.181 3403 Planarity : 0.004 0.052 3593 Dihedral : 12.843 151.587 3059 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 7.40 % Allowed : 24.91 % Favored : 67.69 % 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: 2518 helix: 1.01 (0.15), residues: 1232 sheet: 0.02 (0.23), residues: 516 loop : -0.73 (0.23), residues: 770 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 282 time to evaluate : 2.411 Fit side-chains revert: symmetry clash outliers start: 172 outliers final: 95 residues processed: 408 average time/residue: 1.0935 time to fit residues: 519.8460 Evaluate side-chains 354 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 259 time to evaluate : 2.340 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 75 residues processed: 21 average time/residue: 0.3306 time to fit residues: 13.9842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 157 optimal weight: 0.0030 chunk 63 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN C 298 HIS D 24 GLN D 207 GLN D 352 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 291 HIS G 190 ASN G 268 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21629 Z= 0.181 Angle : 0.531 9.344 29334 Z= 0.273 Chirality : 0.041 0.186 3403 Planarity : 0.004 0.045 3593 Dihedral : 12.685 133.798 3059 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.37 % Allowed : 26.08 % Favored : 67.56 % 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: 0.54 (0.17), residues: 2518 helix: 1.18 (0.15), residues: 1226 sheet: 0.10 (0.23), residues: 519 loop : -0.64 (0.23), residues: 773 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 286 time to evaluate : 2.480 Fit side-chains revert: symmetry clash outliers start: 148 outliers final: 93 residues processed: 396 average time/residue: 1.0579 time to fit residues: 491.4003 Evaluate side-chains 355 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 262 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 73 residues processed: 22 average time/residue: 0.3979 time to fit residues: 15.7038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 121 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 298 HIS D 24 GLN D 207 GLN E 18 HIS E 104 ASN F 291 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21629 Z= 0.240 Angle : 0.545 7.957 29334 Z= 0.280 Chirality : 0.042 0.155 3403 Planarity : 0.004 0.050 3593 Dihedral : 12.650 129.793 3059 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.54 % Allowed : 26.03 % Favored : 67.43 % 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: 0.49 (0.17), residues: 2518 helix: 1.11 (0.15), residues: 1230 sheet: 0.12 (0.23), residues: 521 loop : -0.65 (0.23), residues: 767 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 279 time to evaluate : 2.594 Fit side-chains revert: symmetry clash outliers start: 152 outliers final: 96 residues processed: 392 average time/residue: 1.0446 time to fit residues: 482.3104 Evaluate side-chains 360 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 264 time to evaluate : 2.401 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 76 residues processed: 21 average time/residue: 0.4055 time to fit residues: 15.3891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 209 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 125 optimal weight: 0.0030 chunk 220 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 298 HIS C 333 ASN D 24 GLN D 207 GLN E 18 HIS E 104 ASN F 291 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21629 Z= 0.177 Angle : 0.522 12.638 29334 Z= 0.267 Chirality : 0.041 0.158 3403 Planarity : 0.004 0.043 3593 Dihedral : 12.555 121.305 3059 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.90 % Allowed : 27.19 % Favored : 66.91 % 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 (0.17), residues: 2518 helix: 1.27 (0.15), residues: 1221 sheet: 0.19 (0.23), residues: 525 loop : -0.60 (0.23), residues: 772 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 294 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 90 residues processed: 399 average time/residue: 1.0549 time to fit residues: 494.0887 Evaluate side-chains 357 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 267 time to evaluate : 2.319 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 74 residues processed: 17 average time/residue: 0.4247 time to fit residues: 13.5818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 0.6980 chunk 221 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 245 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS C 333 ASN D 24 GLN D 207 GLN E 18 HIS E 104 ASN F 291 HIS H 45 ASN H 53 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21629 Z= 0.268 Angle : 0.565 10.201 29334 Z= 0.289 Chirality : 0.042 0.169 3403 Planarity : 0.004 0.050 3593 Dihedral : 12.585 122.037 3059 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.90 % Allowed : 27.54 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2518 helix: 1.10 (0.15), residues: 1223 sheet: 0.17 (0.23), residues: 526 loop : -0.65 (0.23), residues: 769 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 277 time to evaluate : 2.305 Fit side-chains revert: symmetry clash outliers start: 137 outliers final: 93 residues processed: 380 average time/residue: 1.1209 time to fit residues: 497.4719 Evaluate side-chains 355 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 262 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 77 residues processed: 17 average time/residue: 0.4071 time to fit residues: 13.2140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 139 optimal weight: 0.3980 chunk 206 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 298 GLN A 495 GLN C 298 HIS C 333 ASN D 207 GLN E 18 HIS E 104 ASN F 291 HIS H 233 ASN H 259 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21629 Z= 0.308 Angle : 0.589 9.684 29334 Z= 0.302 Chirality : 0.043 0.177 3403 Planarity : 0.004 0.039 3593 Dihedral : 12.673 122.834 3059 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.02 % Allowed : 27.58 % Favored : 66.39 % 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: 2518 helix: 0.98 (0.15), residues: 1214 sheet: 0.03 (0.23), residues: 546 loop : -0.66 (0.23), residues: 758 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 270 time to evaluate : 2.395 Fit side-chains revert: symmetry clash outliers start: 140 outliers final: 99 residues processed: 378 average time/residue: 1.1076 time to fit residues: 492.1086 Evaluate side-chains 359 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 260 time to evaluate : 2.272 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 81 residues processed: 19 average time/residue: 0.5527 time to fit residues: 17.1297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 192 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN C 298 HIS C 333 ASN E 18 HIS E 104 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21629 Z= 0.182 Angle : 0.534 12.476 29334 Z= 0.274 Chirality : 0.041 0.200 3403 Planarity : 0.004 0.046 3593 Dihedral : 12.521 111.783 3059 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.82 % Allowed : 28.79 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2518 helix: 1.18 (0.15), residues: 1219 sheet: 0.17 (0.23), residues: 526 loop : -0.63 (0.23), residues: 773 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 276 time to evaluate : 2.482 Fit side-chains revert: symmetry clash outliers start: 112 outliers final: 86 residues processed: 370 average time/residue: 1.1114 time to fit residues: 482.0173 Evaluate side-chains 355 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 269 time to evaluate : 2.406 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 75 residues processed: 13 average time/residue: 0.3953 time to fit residues: 11.0123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 179 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 215 optimal weight: 0.0980 chunk 227 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 417 ASN B 8 GLN C 298 HIS C 333 ASN D 207 GLN E 18 HIS E 104 ASN E 292 HIS F 291 HIS H 245 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 21629 Z= 0.451 Angle : 0.688 14.743 29334 Z= 0.349 Chirality : 0.047 0.210 3403 Planarity : 0.005 0.074 3593 Dihedral : 12.733 123.168 3059 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.08 % Allowed : 28.66 % Favored : 66.27 % 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: 0.01 (0.17), residues: 2518 helix: 0.65 (0.15), residues: 1216 sheet: -0.05 (0.23), residues: 546 loop : -0.81 (0.23), residues: 756 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 264 time to evaluate : 2.331 Fit side-chains revert: symmetry clash outliers start: 118 outliers final: 88 residues processed: 362 average time/residue: 1.1553 time to fit residues: 487.4615 Evaluate side-chains 337 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 249 time to evaluate : 2.476 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 78 residues processed: 11 average time/residue: 0.5301 time to fit residues: 11.1641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 0.5980 chunk 241 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 167 optimal weight: 0.3980 chunk 253 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 123 optimal weight: 0.4980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN C 298 HIS E 104 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21629 Z= 0.183 Angle : 0.559 13.343 29334 Z= 0.286 Chirality : 0.041 0.158 3403 Planarity : 0.004 0.039 3593 Dihedral : 12.497 109.626 3059 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.09 % Allowed : 29.78 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2518 helix: 1.00 (0.15), residues: 1220 sheet: 0.09 (0.23), residues: 534 loop : -0.67 (0.23), residues: 764 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5036 Ramachandran restraints generated. 2518 Oldfield, 0 Emsley, 2518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 259 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 74 residues processed: 344 average time/residue: 1.0676 time to fit residues: 433.3826 Evaluate side-chains 324 residues out of total 2326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 250 time to evaluate : 2.694 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 72 residues processed: 3 average time/residue: 0.2374 time to fit residues: 4.6986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN C 298 HIS C 333 ASN E 104 ASN F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.198497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149427 restraints weight = 23764.796| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.09 r_work: 0.3499 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21629 Z= 0.326 Angle : 0.618 13.988 29334 Z= 0.314 Chirality : 0.044 0.206 3403 Planarity : 0.004 0.044 3593 Dihedral : 12.543 111.128 3059 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.13 % Allowed : 29.86 % Favored : 66.01 % 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: 0.25 (0.17), residues: 2518 helix: 0.87 (0.15), residues: 1221 sheet: 0.09 (0.23), residues: 538 loop : -0.76 (0.23), residues: 759 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8228.58 seconds wall clock time: 148 minutes 59.56 seconds (8939.56 seconds total)