Starting phenix.real_space_refine (version: dev) on Mon Dec 12 07:22:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2022/6ta3_10421_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2022/6ta3_10421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2022/6ta3_10421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2022/6ta3_10421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2022/6ta3_10421_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/12_2022/6ta3_10421_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B ASP 355": "OD1" <-> "OD2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A ASP 39": "OD1" <-> "OD2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "K PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 32": "OE1" <-> "OE2" Residue "K ASP 59": "OD1" <-> "OD2" Residue "K PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 69": "OD1" <-> "OD2" Residue "K TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 153": "OE1" <-> "OE2" Residue "K ASP 177": "OD1" <-> "OD2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K ASP 187": "OD1" <-> "OD2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K GLU 200": "OE1" <-> "OE2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "K ASP 208": "OD1" <-> "OD2" Residue "K TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 234": "NH1" <-> "NH2" Residue "K ASP 265": "OD1" <-> "OD2" Residue "K ASP 279": "OD1" <-> "OD2" Residue "K GLU 284": "OE1" <-> "OE2" Residue "K ARG 327": "NH1" <-> "NH2" Residue "K GLU 344": "OE1" <-> "OE2" Residue "K GLU 351": "OE1" <-> "OE2" Residue "K TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3372 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Chain: "A" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3425 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 415} Chain: "K" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2607 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 322} Chain breaks: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'MZK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.87, per 1000 atoms: 0.62 Number of scatterers: 9491 At special positions: 0 Unit cell: (70.85, 103.55, 111.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1833 8.00 N 1637 7.00 C 5952 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 12 sheets defined 46.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.857A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 101 through 126 removed outlier: 4.282A pdb=" N ALA B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 158 removed outlier: 3.567A pdb=" N LEU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 removed outlier: 4.045A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 222 through 241 removed outlier: 3.618A pdb=" N VAL B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 286 through 294 removed outlier: 4.281A pdb=" N THR B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 323 through 336 removed outlier: 3.539A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 405 through 427 removed outlier: 3.782A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.516A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 86' Processing helix chain 'A' and resid 103 through 128 removed outlier: 4.339A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 Processing helix chain 'A' and resid 181 through 197 removed outlier: 4.027A pdb=" N TYR A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 243 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.956A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'K' and resid 30 through 35 Processing helix chain 'K' and resid 78 through 95 removed outlier: 3.695A pdb=" N CYS K 87 " --> pdb=" O ARG K 83 " (cutoff:3.500A) Proline residue: K 88 - end of helix removed outlier: 3.503A pdb=" N GLU K 92 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 116 Processing helix chain 'K' and resid 136 through 150 removed outlier: 3.601A pdb=" N LEU K 140 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS K 141 " --> pdb=" O PRO K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 221 removed outlier: 3.621A pdb=" N ALA K 219 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS K 220 " --> pdb=" O LYS K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 275 No H-bonds generated for 'chain 'K' and resid 272 through 275' Processing helix chain 'K' and resid 279 through 304 Processing helix chain 'K' and resid 311 through 313 No H-bonds generated for 'chain 'K' and resid 311 through 313' Processing helix chain 'K' and resid 315 through 319 Processing helix chain 'K' and resid 321 through 323 No H-bonds generated for 'chain 'K' and resid 321 through 323' Processing helix chain 'K' and resid 343 through 358 removed outlier: 3.542A pdb=" N LYS K 357 " --> pdb=" O ALA K 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN K 358 " --> pdb=" O HIS K 354 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 63 through 65 removed outlier: 7.223A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 170 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 202 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'B' and resid 267 through 270 removed outlier: 3.527A pdb=" N GLY B 369 " --> pdb=" O MET B 267 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 314 through 317 removed outlier: 6.073A pdb=" N LYS B 350 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE B 317 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA B 352 " --> pdb=" O PHE B 317 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= F, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= G, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.841A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= I, first strand: chain 'K' and resid 70 through 72 removed outlier: 3.669A pdb=" N MET K 70 " --> pdb=" O VAL K 21 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N CYS K 99 " --> pdb=" O ILE K 258 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS K 260 " --> pdb=" O CYS K 99 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE K 101 " --> pdb=" O LYS K 260 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN K 262 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA K 103 " --> pdb=" O ASN K 262 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL K 264 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N GLY K 105 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL K 158 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE K 202 " --> pdb=" O VAL K 158 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 42 through 44 Processing sheet with id= K, first strand: chain 'K' and resid 161 through 164 Processing sheet with id= L, first strand: chain 'K' and resid 183 through 186 removed outlier: 4.264A pdb=" N GLN K 183 " --> pdb=" O LYS K 197 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1260 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: 2.86 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.91: 1 0.91 - 1.14: 3 1.14 - 1.36: 3087 1.36 - 1.59: 6495 1.59 - 1.82: 95 Bond restraints: 9681 Sorted by residual: bond pdb=" CB SER K 84 " pdb=" OG SER K 84 " ideal model delta sigma weight residual 1.417 0.678 0.739 2.00e-02 2.50e+03 1.37e+03 bond pdb=" CB GLU K 254 " pdb=" CG GLU K 254 " ideal model delta sigma weight residual 1.520 1.061 0.459 3.00e-02 1.11e+03 2.35e+02 bond pdb=" C3A G2P A 501 " pdb=" PB G2P A 501 " ideal model delta sigma weight residual 1.850 1.591 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C THR K 306 " pdb=" O THR K 306 " ideal model delta sigma weight residual 1.234 1.083 0.151 1.26e-02 6.30e+03 1.43e+02 bond pdb=" C3A G2P A 501 " pdb=" PA G2P A 501 " ideal model delta sigma weight residual 1.818 1.592 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 9676 not shown) Histogram of bond angle deviations from ideal: 90.86 - 102.48: 46 102.48 - 114.09: 5889 114.09 - 125.71: 7091 125.71 - 137.32: 99 137.32 - 148.93: 3 Bond angle restraints: 13128 Sorted by residual: angle pdb=" CA GLY B 10 " pdb=" C GLY B 10 " pdb=" N GLN B 11 " ideal model delta sigma weight residual 115.13 148.93 -33.80 1.05e+00 9.07e-01 1.04e+03 angle pdb=" O GLY B 10 " pdb=" C GLY B 10 " pdb=" N GLN B 11 " ideal model delta sigma weight residual 122.56 90.86 31.70 1.15e+00 7.56e-01 7.60e+02 angle pdb=" CA SER K 84 " pdb=" CB SER K 84 " pdb=" OG SER K 84 " ideal model delta sigma weight residual 111.10 139.29 -28.19 2.00e+00 2.50e-01 1.99e+02 angle pdb=" CA GLU K 254 " pdb=" CB GLU K 254 " pdb=" CG GLU K 254 " ideal model delta sigma weight residual 114.10 139.62 -25.52 2.00e+00 2.50e-01 1.63e+02 angle pdb=" N ASN K 289 " pdb=" CA ASN K 289 " pdb=" C ASN K 289 " ideal model delta sigma weight residual 111.07 99.23 11.84 1.07e+00 8.73e-01 1.22e+02 ... (remaining 13123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.36: 5025 18.36 - 36.72: 493 36.72 - 55.08: 178 55.08 - 73.44: 80 73.44 - 91.80: 14 Dihedral angle restraints: 5790 sinusoidal: 2325 harmonic: 3465 Sorted by residual: dihedral pdb=" CA GLY K 110 " pdb=" C GLY K 110 " pdb=" N LYS K 111 " pdb=" CA LYS K 111 " ideal model delta harmonic sigma weight residual 180.00 137.42 42.58 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA GLN B 15 " pdb=" C GLN B 15 " pdb=" N ILE B 16 " pdb=" CA ILE B 16 " ideal model delta harmonic sigma weight residual -180.00 -146.07 -33.93 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" N THR B 143 " pdb=" C THR B 143 " pdb=" CA THR B 143 " pdb=" CB THR B 143 " ideal model delta harmonic sigma weight residual 123.40 138.49 -15.09 0 2.50e+00 1.60e-01 3.64e+01 ... (remaining 5787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1413 0.183 - 0.365: 43 0.365 - 0.548: 3 0.548 - 0.731: 1 0.731 - 0.913: 1 Chirality restraints: 1461 Sorted by residual: chirality pdb=" CG LEU K 266 " pdb=" CB LEU K 266 " pdb=" CD1 LEU K 266 " pdb=" CD2 LEU K 266 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CA THR B 143 " pdb=" N THR B 143 " pdb=" C THR B 143 " pdb=" CB THR B 143 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA PRO K 137 " pdb=" N PRO K 137 " pdb=" C PRO K 137 " pdb=" CB PRO K 137 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.48 2.00e-01 2.50e+01 5.87e+00 ... (remaining 1458 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 399 " -0.268 2.00e-02 2.50e+03 1.90e-01 7.21e+02 pdb=" CG TYR A 399 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 399 " 0.091 2.00e-02 2.50e+03 pdb=" CD2 TYR A 399 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR A 399 " 0.170 2.00e-02 2.50e+03 pdb=" CE2 TYR A 399 " 0.155 2.00e-02 2.50e+03 pdb=" CZ TYR A 399 " 0.109 2.00e-02 2.50e+03 pdb=" OH TYR A 399 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 345 " -0.043 2.00e-02 2.50e+03 9.65e-02 9.30e+01 pdb=" CD GLU K 345 " 0.167 2.00e-02 2.50e+03 pdb=" OE1 GLU K 345 " -0.063 2.00e-02 2.50e+03 pdb=" OE2 GLU K 345 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 104 " -0.128 2.00e-02 2.50e+03 6.80e-02 9.24e+01 pdb=" CG TYR K 104 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR K 104 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR K 104 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR K 104 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR K 104 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR K 104 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR K 104 " -0.085 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 0.32 - 1.23: 18 1.23 - 2.15: 113 2.15 - 3.07: 11961 3.07 - 3.98: 31684 3.98 - 4.90: 54033 Warning: very small nonbonded interaction distances. Nonbonded interactions: 97809 Sorted by model distance: nonbonded pdb=" NE ARG B 251 " pdb=" CB ALA A 100 " model vdw 0.317 3.540 nonbonded pdb=" OD1 ASN B 99 " pdb=" PG G2P B 501 " model vdw 0.439 2.720 nonbonded pdb=" O PRO B 259 " pdb=" CD1 PHE A 404 " model vdw 0.578 3.340 nonbonded pdb=" NZ LYS B 350 " pdb=" CA THR A 179 " model vdw 0.589 3.550 nonbonded pdb=" NZ LYS B 324 " pdb=" CB ARG A 221 " model vdw 0.616 3.520 ... (remaining 97804 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5952 2.51 5 N 1637 2.21 5 O 1833 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.640 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 30.230 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4896 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 : 0.024 0.739 9681 Z= 1.645 Angle : 2.453 33.803 13128 Z= 1.751 Chirality : 0.078 0.913 1461 Planarity : 0.013 0.190 1703 Dihedral : 18.763 91.805 3564 Min Nonbonded Distance : 0.317 Molprobity Statistics. All-atom Clashscore : 210.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 16.02 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.86 (0.22), residues: 1191 helix: 2.57 (0.20), residues: 558 sheet: 1.18 (0.37), residues: 171 loop : -0.45 (0.23), residues: 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 208 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 67 residues processed: 337 average time/residue: 0.2913 time to fit residues: 125.4994 Evaluate side-chains 173 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 106 time to evaluate : 1.058 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 6 residues processed: 67 average time/residue: 0.2257 time to fit residues: 21.4619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5033 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.105 9681 Z= 0.448 Angle : 1.066 16.134 13128 Z= 0.563 Chirality : 0.058 0.419 1461 Planarity : 0.011 0.240 1703 Dihedral : 8.432 88.976 1321 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 53.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 6.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.00 (0.22), residues: 1191 helix: 0.14 (0.19), residues: 555 sheet: 1.28 (0.36), residues: 194 loop : -0.62 (0.27), residues: 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 163 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 26 residues processed: 213 average time/residue: 0.2377 time to fit residues: 68.9211 Evaluate side-chains 148 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.210 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 2 residues processed: 26 average time/residue: 0.1733 time to fit residues: 8.1135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5178 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 9681 Z= 0.358 Angle : 0.901 17.526 13128 Z= 0.465 Chirality : 0.051 0.352 1461 Planarity : 0.008 0.086 1703 Dihedral : 7.753 86.212 1321 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 40.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 5.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1191 helix: -0.09 (0.20), residues: 546 sheet: 0.72 (0.36), residues: 200 loop : -0.42 (0.29), residues: 445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 24 residues processed: 173 average time/residue: 0.2230 time to fit residues: 53.8711 Evaluate side-chains 141 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.142 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 2 residues processed: 24 average time/residue: 0.1331 time to fit residues: 6.6521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5175 moved from start: 0.7821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 9681 Z= 0.281 Angle : 0.822 17.484 13128 Z= 0.413 Chirality : 0.047 0.272 1461 Planarity : 0.007 0.084 1703 Dihedral : 7.326 82.102 1321 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 35.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1191 helix: 0.05 (0.20), residues: 547 sheet: 0.49 (0.36), residues: 201 loop : -0.49 (0.28), residues: 443 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 165 average time/residue: 0.2162 time to fit residues: 50.4488 Evaluate side-chains 138 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.207 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 0.1243 time to fit residues: 5.0213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5188 moved from start: 0.8377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 9681 Z= 0.245 Angle : 0.771 17.421 13128 Z= 0.389 Chirality : 0.046 0.368 1461 Planarity : 0.006 0.080 1703 Dihedral : 7.142 78.415 1321 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 32.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.24 (0.23), residues: 1191 helix: 0.09 (0.21), residues: 547 sheet: 0.36 (0.36), residues: 201 loop : -0.54 (0.29), residues: 443 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 135 average time/residue: 0.1979 time to fit residues: 39.2071 Evaluate side-chains 119 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 1.144 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.1063 time to fit residues: 3.5728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 moved from start: 0.8776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 9681 Z= 0.239 Angle : 0.769 17.400 13128 Z= 0.385 Chirality : 0.046 0.365 1461 Planarity : 0.006 0.078 1703 Dihedral : 6.979 73.532 1321 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 31.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.20 (0.23), residues: 1191 helix: 0.17 (0.21), residues: 559 sheet: 0.44 (0.36), residues: 201 loop : -0.64 (0.29), residues: 431 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 138 average time/residue: 0.2196 time to fit residues: 43.1697 Evaluate side-chains 121 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.200 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.1065 time to fit residues: 3.3143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 300 ASN K 173 ASN ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5287 moved from start: 0.9128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 9681 Z= 0.288 Angle : 0.781 17.258 13128 Z= 0.395 Chirality : 0.045 0.359 1461 Planarity : 0.006 0.081 1703 Dihedral : 6.893 69.066 1321 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 32.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.19 (0.23), residues: 1191 helix: 0.18 (0.21), residues: 555 sheet: 0.56 (0.37), residues: 193 loop : -0.68 (0.29), residues: 443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 134 average time/residue: 0.2044 time to fit residues: 39.6953 Evaluate side-chains 122 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.121 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.1011 time to fit residues: 3.7219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 22 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS B 226 ASN B 245 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5284 moved from start: 0.9598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9681 Z= 0.256 Angle : 0.790 17.444 13128 Z= 0.392 Chirality : 0.046 0.350 1461 Planarity : 0.006 0.096 1703 Dihedral : 6.832 66.279 1321 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 29.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.15 (0.23), residues: 1191 helix: 0.24 (0.21), residues: 556 sheet: 0.56 (0.37), residues: 191 loop : -0.67 (0.29), residues: 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 130 average time/residue: 0.2126 time to fit residues: 39.9122 Evaluate side-chains 115 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.312 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1076 time to fit residues: 3.6022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.0970 chunk 99 optimal weight: 0.0570 chunk 105 optimal weight: 0.0770 chunk 63 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 moved from start: 0.9895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 9681 Z= 0.239 Angle : 0.790 17.243 13128 Z= 0.392 Chirality : 0.046 0.408 1461 Planarity : 0.006 0.093 1703 Dihedral : 6.629 65.205 1321 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 27.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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 (0.23), residues: 1191 helix: 0.29 (0.21), residues: 558 sheet: 0.66 (0.38), residues: 184 loop : -0.75 (0.28), residues: 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 120 average time/residue: 0.2299 time to fit residues: 38.6925 Evaluate side-chains 108 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.024 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1090 time to fit residues: 3.0600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.0070 chunk 77 optimal weight: 0.0970 chunk 117 optimal weight: 0.0030 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.0670 chunk 99 optimal weight: 0.5980 overall best weight: 0.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5214 moved from start: 1.0097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 9681 Z= 0.229 Angle : 0.793 17.466 13128 Z= 0.388 Chirality : 0.045 0.279 1461 Planarity : 0.006 0.090 1703 Dihedral : 6.472 62.612 1321 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 26.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.12 (0.23), residues: 1191 helix: 0.24 (0.21), residues: 569 sheet: 0.75 (0.38), residues: 190 loop : -0.75 (0.28), residues: 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.2281 time to fit residues: 36.6211 Evaluate side-chains 106 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 1.171 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2086 time to fit residues: 2.4612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 17 optimal weight: 0.0030 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.084711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.069808 restraints weight = 44718.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.071892 restraints weight = 25753.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.073285 restraints weight = 17138.459| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 1.0319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 9681 Z= 0.251 Angle : 0.788 17.062 13128 Z= 0.388 Chirality : 0.045 0.267 1461 Planarity : 0.006 0.085 1703 Dihedral : 6.378 55.722 1321 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 27.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.26 % 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: -0.05 (0.23), residues: 1191 helix: 0.39 (0.21), residues: 566 sheet: 0.67 (0.38), residues: 189 loop : -0.79 (0.27), residues: 436 =============================================================================== Job complete usr+sys time: 2415.15 seconds wall clock time: 44 minutes 53.44 seconds (2693.44 seconds total)