Starting phenix.real_space_refine on Thu Mar 14 18:47:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/03_2024/6ta3_10421_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/03_2024/6ta3_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_10421/03_2024/6ta3_10421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/03_2024/6ta3_10421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/03_2024/6ta3_10421_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ta3_10421/03_2024/6ta3_10421_updated.pdb" } resolution = 3.8 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= 0.000 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 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. 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-5265/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: 5.57, per 1000 atoms: 0.59 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: 5.17 Conformation dependent library (CDL) restraints added in 1.7 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: 2.04 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: 3.01 Time building geometry restraints manager: 5.40 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: 5060 18.36 - 36.72: 507 36.72 - 55.08: 182 55.08 - 73.44: 86 73.44 - 91.80: 15 Dihedral angle restraints: 5850 sinusoidal: 2385 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 5847 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 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: 5.330 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: 26.330 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 31.130 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5093 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 : 18.955 91.805 3624 Min Nonbonded Distance : 0.317 Molprobity Statistics. All-atom Clashscore : 210.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 16.02 % Allowed : 16.99 % Favored : 66.99 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP B 344 HIS 0.004 0.000 HIS K 354 PHE 0.033 0.002 PHE K 113 TYR 0.369 0.011 TYR A 399 ARG 0.086 0.002 ARG A 402 *********************** 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 : 1.150 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 REVERT: B 122 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7780 (mttt) REVERT: B 210 ILE cc_start: 0.8044 (mt) cc_final: 0.7747 (mm) REVERT: B 293 MET cc_start: 0.6417 (mtp) cc_final: 0.6210 (mtp) REVERT: B 336 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7157 (mttt) REVERT: B 359 ARG cc_start: 0.6333 (mtt180) cc_final: 0.4900 (mtt180) REVERT: A 22 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: A 164 LYS cc_start: 0.4698 (OUTLIER) cc_final: 0.3022 (mmtp) REVERT: A 212 ILE cc_start: 0.8030 (mm) cc_final: 0.7747 (mm) REVERT: A 220 GLU cc_start: 0.3323 (OUTLIER) cc_final: 0.2577 (pp20) REVERT: A 266 HIS cc_start: 0.6925 (m90) cc_final: 0.6330 (m90) REVERT: A 303 VAL cc_start: 0.8192 (p) cc_final: 0.7169 (p) REVERT: A 396 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7716 (t0) outliers start: 165 outliers final: 67 residues processed: 337 average time/residue: 0.3043 time to fit residues: 130.1139 Evaluate side-chains 182 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 109 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 ** 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 176 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 233 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5235 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 9681 Z= 0.432 Angle : 1.052 16.805 13128 Z= 0.550 Chirality : 0.057 0.386 1461 Planarity : 0.010 0.152 1703 Dihedral : 15.370 89.864 1588 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 49.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 11.07 % Allowed : 22.14 % Favored : 66.80 % 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: -0.04 (0.22), residues: 1191 helix: 0.07 (0.19), residues: 557 sheet: 1.20 (0.36), residues: 195 loop : -0.56 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 21 HIS 0.013 0.003 HIS A 393 PHE 0.039 0.003 PHE B 385 TYR 0.143 0.004 TYR A 224 ARG 0.009 0.001 ARG B 251 *********************** 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 278 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 164 time to evaluate : 1.153 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: B 3 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5784 (mm-30) REVERT: B 22 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6951 (pp20) REVERT: B 23 VAL cc_start: 0.8569 (p) cc_final: 0.8168 (p) REVERT: B 31 ASP cc_start: 0.4100 (OUTLIER) cc_final: 0.3698 (t0) REVERT: B 147 MET cc_start: 0.7358 (pmm) cc_final: 0.6951 (pmm) REVERT: B 154 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8778 (ttpp) REVERT: B 155 ILE cc_start: 0.7436 (pt) cc_final: 0.7013 (tp) REVERT: B 158 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5383 (mp0) REVERT: B 280 GLN cc_start: 0.7152 (pt0) cc_final: 0.6910 (pt0) REVERT: B 293 MET cc_start: 0.7419 (mtp) cc_final: 0.7192 (ptt) REVERT: B 336 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8150 (mttt) REVERT: A 52 PHE cc_start: 0.6414 (m-10) cc_final: 0.5824 (m-10) REVERT: A 164 LYS cc_start: 0.4913 (OUTLIER) cc_final: 0.4423 (tppt) REVERT: A 204 VAL cc_start: 0.3985 (OUTLIER) cc_final: 0.3643 (p) REVERT: A 212 ILE cc_start: 0.8277 (mm) cc_final: 0.7986 (pt) REVERT: A 242 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4690 (tm) REVERT: A 338 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7760 (tppp) REVERT: A 371 VAL cc_start: 0.4080 (OUTLIER) cc_final: 0.3754 (t) outliers start: 114 outliers final: 54 residues processed: 251 average time/residue: 0.2739 time to fit residues: 89.8970 Evaluate side-chains 181 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 117 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 342 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.3980 chunk 33 optimal weight: 0.0170 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5289 moved from start: 0.6898 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= 0.301 Angle : 0.859 16.540 13128 Z= 0.439 Chirality : 0.047 0.318 1461 Planarity : 0.007 0.073 1703 Dihedral : 13.024 89.106 1493 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 38.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 9.51 % Allowed : 23.20 % Favored : 67.28 % 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: -0.11 (0.23), residues: 1191 helix: 0.13 (0.20), residues: 548 sheet: 0.80 (0.36), residues: 193 loop : -0.55 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 21 HIS 0.010 0.002 HIS B 105 PHE 0.026 0.003 PHE B 385 TYR 0.147 0.003 TYR A 224 ARG 0.010 0.001 ARG K 33 *********************** 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 239 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 141 time to evaluate : 1.168 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: B 3 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5501 (mm-30) REVERT: B 31 ASP cc_start: 0.4187 (OUTLIER) cc_final: 0.3748 (p0) REVERT: B 155 ILE cc_start: 0.7728 (pt) cc_final: 0.7502 (mm) REVERT: B 187 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7933 (mm) REVERT: B 280 GLN cc_start: 0.6829 (pt0) cc_final: 0.6075 (pt0) REVERT: B 293 MET cc_start: 0.7454 (mtp) cc_final: 0.7238 (ptt) REVERT: B 336 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7894 (mttt) REVERT: A 52 PHE cc_start: 0.6331 (m-10) cc_final: 0.5823 (m-10) REVERT: A 154 MET cc_start: 0.6698 (tpp) cc_final: 0.6474 (tpp) REVERT: A 164 LYS cc_start: 0.4975 (OUTLIER) cc_final: 0.4738 (mmtp) REVERT: A 212 ILE cc_start: 0.8222 (mm) cc_final: 0.7919 (mm) REVERT: A 242 LEU cc_start: 0.4609 (OUTLIER) cc_final: 0.4200 (tm) REVERT: A 267 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5278 (p90) REVERT: A 388 TRP cc_start: 0.8599 (m-10) cc_final: 0.8317 (m-90) REVERT: A 432 TYR cc_start: 0.6476 (OUTLIER) cc_final: 0.5712 (t80) outliers start: 98 outliers final: 54 residues processed: 205 average time/residue: 0.2450 time to fit residues: 68.2319 Evaluate side-chains 178 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 116 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN B 134 GLN ** 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 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN A 176 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 moved from start: 0.7869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9681 Z= 0.289 Angle : 0.801 16.444 13128 Z= 0.410 Chirality : 0.045 0.296 1461 Planarity : 0.007 0.077 1703 Dihedral : 12.106 94.589 1461 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 34.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 8.25 % Allowed : 24.56 % Favored : 67.18 % 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: -0.06 (0.23), residues: 1191 helix: 0.21 (0.20), residues: 545 sheet: 0.62 (0.36), residues: 201 loop : -0.51 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP B 21 HIS 0.010 0.002 HIS B 105 PHE 0.028 0.003 PHE K 68 TYR 0.140 0.003 TYR A 224 ARG 0.007 0.001 ARG B 262 *********************** 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 210 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 125 time to evaluate : 1.110 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: B 31 ASP cc_start: 0.4747 (OUTLIER) cc_final: 0.4264 (t0) REVERT: B 103 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7475 (mttp) REVERT: B 257 MET cc_start: 0.8241 (tpp) cc_final: 0.7905 (tpt) REVERT: B 280 GLN cc_start: 0.6987 (pt0) cc_final: 0.6346 (pp30) REVERT: B 293 MET cc_start: 0.7390 (mtp) cc_final: 0.7109 (ptt) REVERT: B 336 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7867 (mttt) REVERT: A 52 PHE cc_start: 0.6230 (m-10) cc_final: 0.5690 (m-10) REVERT: A 150 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8200 (m) REVERT: A 212 ILE cc_start: 0.8295 (mm) cc_final: 0.7917 (mm) REVERT: A 242 LEU cc_start: 0.4558 (OUTLIER) cc_final: 0.3622 (tt) REVERT: A 267 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.5628 (p90) REVERT: A 313 MET cc_start: 0.5163 (mtp) cc_final: 0.4882 (mtt) REVERT: A 388 TRP cc_start: 0.8413 (m-10) cc_final: 0.8012 (m-90) REVERT: A 432 TYR cc_start: 0.6654 (OUTLIER) cc_final: 0.5833 (t80) outliers start: 85 outliers final: 49 residues processed: 185 average time/residue: 0.2584 time to fit residues: 63.5354 Evaluate side-chains 168 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 112 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.6980 chunk 64 optimal weight: 0.0020 chunk 1 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 0.8487 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= 0.257 Angle : 0.752 16.355 13128 Z= 0.383 Chirality : 0.044 0.241 1461 Planarity : 0.006 0.086 1703 Dihedral : 11.366 94.104 1439 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 31.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 6.50 % Allowed : 25.83 % Favored : 67.67 % 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: 0.01 (0.23), residues: 1191 helix: 0.36 (0.21), residues: 553 sheet: 0.47 (0.36), residues: 203 loop : -0.50 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 21 HIS 0.009 0.002 HIS B 105 PHE 0.035 0.002 PHE K 68 TYR 0.140 0.003 TYR A 224 ARG 0.009 0.001 ARG B 251 *********************** 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 190 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 123 time to evaluate : 1.172 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: B 31 ASP cc_start: 0.4901 (OUTLIER) cc_final: 0.4327 (t0) REVERT: B 103 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7740 (tmtt) REVERT: B 257 MET cc_start: 0.8295 (tpp) cc_final: 0.8067 (tpt) REVERT: B 280 GLN cc_start: 0.6694 (pt0) cc_final: 0.6320 (pp30) REVERT: B 293 MET cc_start: 0.7458 (mtp) cc_final: 0.7007 (ptt) REVERT: B 336 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7970 (mtmm) REVERT: B 375 GLN cc_start: 0.4869 (OUTLIER) cc_final: 0.4550 (mp10) REVERT: A 52 PHE cc_start: 0.6278 (m-10) cc_final: 0.6058 (m-10) REVERT: A 212 ILE cc_start: 0.8340 (mm) cc_final: 0.7978 (mm) REVERT: A 267 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5656 (p90) REVERT: A 313 MET cc_start: 0.5073 (mtp) cc_final: 0.4747 (mtt) REVERT: A 373 ARG cc_start: 0.7437 (mpt180) cc_final: 0.7122 (mtt180) REVERT: A 432 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5834 (t80) outliers start: 67 outliers final: 42 residues processed: 165 average time/residue: 0.2442 time to fit residues: 54.4413 Evaluate side-chains 159 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 111 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 8 GLN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 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: 0.5523 moved from start: 0.9025 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= 0.269 Angle : 0.749 16.329 13128 Z= 0.381 Chirality : 0.044 0.208 1461 Planarity : 0.006 0.091 1703 Dihedral : 10.815 96.495 1427 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 31.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 7.38 % Allowed : 24.95 % Favored : 67.67 % 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 (0.24), residues: 1191 helix: 0.48 (0.21), residues: 557 sheet: 0.51 (0.37), residues: 194 loop : -0.63 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 21 HIS 0.010 0.002 HIS A 406 PHE 0.027 0.002 PHE B 378 TYR 0.139 0.003 TYR A 224 ARG 0.008 0.001 ARG B 241 *********************** 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 195 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 119 time to evaluate : 1.186 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: B 31 ASP cc_start: 0.4460 (OUTLIER) cc_final: 0.4126 (p0) REVERT: B 103 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7728 (tmtt) REVERT: B 257 MET cc_start: 0.8360 (tpp) cc_final: 0.8100 (tpt) REVERT: B 293 MET cc_start: 0.7684 (mtp) cc_final: 0.7125 (ptt) REVERT: B 331 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8291 (pp) REVERT: A 52 PHE cc_start: 0.6455 (m-10) cc_final: 0.6178 (m-10) REVERT: A 212 ILE cc_start: 0.8383 (mm) cc_final: 0.8079 (mm) REVERT: A 242 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.3724 (tt) REVERT: A 267 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.5715 (p90) REVERT: A 313 MET cc_start: 0.5174 (mtp) cc_final: 0.4809 (mtt) REVERT: A 373 ARG cc_start: 0.7573 (mpt180) cc_final: 0.7313 (mtt180) REVERT: A 432 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.5796 (t80) outliers start: 76 outliers final: 47 residues processed: 174 average time/residue: 0.2284 time to fit residues: 54.3557 Evaluate side-chains 161 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 108 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.0030 chunk 52 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.9399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9681 Z= 0.263 Angle : 0.759 17.979 13128 Z= 0.389 Chirality : 0.043 0.197 1461 Planarity : 0.006 0.094 1703 Dihedral : 10.908 97.281 1418 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 30.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 6.60 % Allowed : 25.73 % Favored : 67.67 % 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: 0.04 (0.24), residues: 1191 helix: 0.53 (0.21), residues: 557 sheet: 0.41 (0.37), residues: 196 loop : -0.68 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 21 HIS 0.017 0.002 HIS B 28 PHE 0.020 0.002 PHE B 385 TYR 0.182 0.003 TYR A 224 ARG 0.006 0.001 ARG B 241 *********************** 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 183 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 115 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 revert: symmetry clash REVERT: B 31 ASP cc_start: 0.4354 (OUTLIER) cc_final: 0.4070 (p0) REVERT: B 103 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7727 (tmtt) REVERT: B 257 MET cc_start: 0.8416 (tpp) cc_final: 0.8148 (tpt) REVERT: B 293 MET cc_start: 0.7783 (mtp) cc_final: 0.7226 (ptt) REVERT: B 331 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8187 (pp) REVERT: B 406 MET cc_start: 0.8089 (ptp) cc_final: 0.7885 (ptp) REVERT: A 52 PHE cc_start: 0.6295 (m-10) cc_final: 0.5901 (m-10) REVERT: A 132 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6354 (mt) REVERT: A 203 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5468 (mpp) REVERT: A 212 ILE cc_start: 0.8368 (mm) cc_final: 0.8049 (mm) REVERT: A 267 PHE cc_start: 0.6477 (OUTLIER) cc_final: 0.5854 (p90) REVERT: A 313 MET cc_start: 0.5204 (mtp) cc_final: 0.4926 (mtt) REVERT: A 373 ARG cc_start: 0.7523 (mpt180) cc_final: 0.7287 (mtt180) REVERT: A 432 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.5888 (t80) outliers start: 68 outliers final: 50 residues processed: 161 average time/residue: 0.2411 time to fit residues: 52.9938 Evaluate side-chains 163 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 106 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE 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: 0.1980 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 ASN K 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.9815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9681 Z= 0.248 Angle : 0.753 16.640 13128 Z= 0.380 Chirality : 0.043 0.187 1461 Planarity : 0.006 0.096 1703 Dihedral : 10.679 98.654 1416 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 28.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.89 % Allowed : 26.21 % Favored : 66.89 % 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: 0.01 (0.24), residues: 1191 helix: 0.56 (0.21), residues: 564 sheet: 0.41 (0.37), residues: 197 loop : -0.80 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 21 HIS 0.015 0.002 HIS B 28 PHE 0.038 0.002 PHE B 378 TYR 0.166 0.003 TYR A 224 ARG 0.009 0.001 ARG K 33 *********************** 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 185 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 114 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 revert: symmetry clash revert: symmetry clash REVERT: B 31 ASP cc_start: 0.4133 (OUTLIER) cc_final: 0.3626 (p0) REVERT: B 257 MET cc_start: 0.8438 (tpp) cc_final: 0.8195 (tpt) REVERT: B 293 MET cc_start: 0.7772 (mtp) cc_final: 0.7277 (ptt) REVERT: B 299 MET cc_start: 0.7611 (mmm) cc_final: 0.7359 (tpt) REVERT: B 331 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8216 (pp) REVERT: A 132 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6511 (mt) REVERT: A 212 ILE cc_start: 0.8364 (mm) cc_final: 0.7975 (mm) REVERT: A 220 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6324 (pp20) REVERT: A 267 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.5607 (p90) REVERT: A 313 MET cc_start: 0.5403 (mtp) cc_final: 0.5150 (mtt) REVERT: A 432 TYR cc_start: 0.6579 (OUTLIER) cc_final: 0.5975 (t80) outliers start: 71 outliers final: 48 residues processed: 162 average time/residue: 0.2323 time to fit residues: 51.1953 Evaluate side-chains 160 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 106 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 0.0050 chunk 112 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 1.0055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9681 Z= 0.268 Angle : 0.790 20.071 13128 Z= 0.393 Chirality : 0.044 0.258 1461 Planarity : 0.006 0.096 1703 Dihedral : 10.392 96.351 1408 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 29.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.83 % Allowed : 27.09 % Favored : 67.09 % 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: 0.01 (0.24), residues: 1191 helix: 0.63 (0.21), residues: 563 sheet: 0.33 (0.36), residues: 197 loop : -0.87 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 21 HIS 0.008 0.001 HIS B 105 PHE 0.020 0.002 PHE A 267 TYR 0.195 0.003 TYR A 224 ARG 0.014 0.001 ARG B 46 *********************** 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 174 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 114 time to evaluate : 1.166 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: B 31 ASP cc_start: 0.3951 (OUTLIER) cc_final: 0.3496 (p0) REVERT: B 257 MET cc_start: 0.8439 (tpp) cc_final: 0.8203 (tpt) REVERT: B 293 MET cc_start: 0.7942 (mtp) cc_final: 0.7500 (ptt) REVERT: B 299 MET cc_start: 0.7633 (mmm) cc_final: 0.7361 (tpt) REVERT: B 379 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7998 (tppt) REVERT: A 52 PHE cc_start: 0.5966 (m-10) cc_final: 0.5643 (m-10) REVERT: A 132 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6627 (mt) REVERT: A 212 ILE cc_start: 0.8438 (mm) cc_final: 0.8069 (mm) REVERT: A 220 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6341 (pp20) REVERT: A 267 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.5583 (p90) REVERT: A 313 MET cc_start: 0.5562 (mtp) cc_final: 0.5223 (mtt) REVERT: A 432 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5978 (t80) outliers start: 60 outliers final: 46 residues processed: 155 average time/residue: 0.2361 time to fit residues: 50.0158 Evaluate side-chains 158 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 106 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 38 HIS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 ASN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 1.0351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9681 Z= 0.327 Angle : 0.851 18.909 13128 Z= 0.434 Chirality : 0.047 0.275 1461 Planarity : 0.007 0.102 1703 Dihedral : 10.123 81.152 1405 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 33.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.63 % Allowed : 27.67 % Favored : 66.70 % 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 (0.24), residues: 1191 helix: 0.47 (0.21), residues: 562 sheet: 0.25 (0.36), residues: 200 loop : -0.99 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 101 HIS 0.018 0.002 HIS B 28 PHE 0.056 0.003 PHE B 378 TYR 0.184 0.004 TYR A 224 ARG 0.008 0.001 ARG A 243 ********************** 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 168 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 110 time to evaluate : 1.077 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: B 31 ASP cc_start: 0.4003 (OUTLIER) cc_final: 0.3619 (p0) REVERT: B 257 MET cc_start: 0.8532 (tpp) cc_final: 0.8196 (mmt) REVERT: B 293 MET cc_start: 0.8015 (mtp) cc_final: 0.7456 (tmm) REVERT: A 132 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.6968 (mt) REVERT: A 203 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.6118 (mpp) REVERT: A 212 ILE cc_start: 0.8379 (mm) cc_final: 0.8017 (mm) REVERT: A 267 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.5990 (p90) REVERT: A 313 MET cc_start: 0.5782 (mtp) cc_final: 0.5438 (mtt) REVERT: A 432 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.5944 (t80) outliers start: 58 outliers final: 42 residues processed: 152 average time/residue: 0.2383 time to fit residues: 49.3414 Evaluate side-chains 149 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 102 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 237 SER Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 82 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.081329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.066644 restraints weight = 45093.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.068671 restraints weight = 25417.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.069980 restraints weight = 16662.873| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 1.0590 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= 0.267 Angle : 0.840 18.422 13128 Z= 0.419 Chirality : 0.046 0.245 1461 Planarity : 0.006 0.097 1703 Dihedral : 10.053 80.313 1405 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 30.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.56 % Allowed : 28.93 % Favored : 66.50 % 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: -0.17 (0.24), residues: 1191 helix: 0.48 (0.21), residues: 555 sheet: 0.32 (0.37), residues: 194 loop : -0.96 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 21 HIS 0.023 0.002 HIS B 28 PHE 0.028 0.002 PHE B 378 TYR 0.177 0.003 TYR A 224 ARG 0.016 0.001 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.28 seconds wall clock time: 47 minutes 16.14 seconds (2836.14 seconds total)