Starting phenix.real_space_refine on Sat Feb 17 17:57:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9k_10414/02_2024/6t9k_10414_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9k_10414/02_2024/6t9k_10414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9k_10414/02_2024/6t9k_10414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9k_10414/02_2024/6t9k_10414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9k_10414/02_2024/6t9k_10414_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9k_10414/02_2024/6t9k_10414_neut.pdb" } resolution = 3.3 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= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 12168 2.51 5 N 3341 2.21 5 O 3666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 476": "OD1" <-> "OD2" Residue "D ASP 513": "OD1" <-> "OD2" Residue "D ASP 536": "OD1" <-> "OD2" Residue "D ASP 546": "OD1" <-> "OD2" Residue "D TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 592": "NH1" <-> "NH2" Residue "D TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 613": "OD1" <-> "OD2" Residue "D PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 664": "NH1" <-> "NH2" Residue "D ARG 685": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ASP 744": "OD1" <-> "OD2" Residue "E ASP 19": "OD1" <-> "OD2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 206": "NH1" <-> "NH2" Residue "H ASP 192": "OD1" <-> "OD2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "H ASP 268": "OD1" <-> "OD2" Residue "H GLU 282": "OE1" <-> "OE2" Residue "H ASP 290": "OD1" <-> "OD2" Residue "H ARG 292": "NH1" <-> "NH2" Residue "H GLU 295": "OE1" <-> "OE2" Residue "H ARG 317": "NH1" <-> "NH2" Residue "H ARG 319": "NH1" <-> "NH2" Residue "H ARG 320": "NH1" <-> "NH2" Residue "H TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 344": "OD1" <-> "OD2" Residue "H GLU 361": "OE1" <-> "OE2" Residue "H GLU 398": "OE1" <-> "OE2" Residue "H GLU 401": "OE1" <-> "OE2" Residue "I ARG 421": "NH1" <-> "NH2" Residue "I PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 463": "NH1" <-> "NH2" Residue "I ARG 476": "NH1" <-> "NH2" Residue "I ARG 484": "NH1" <-> "NH2" Residue "I TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K GLU 158": "OE1" <-> "OE2" Residue "K PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 730": "OD1" <-> "OD2" Residue "K GLU 733": "OE1" <-> "OE2" Residue "K GLU 747": "OE1" <-> "OE2" Residue "K GLU 754": "OE1" <-> "OE2" Residue "K GLU 875": "OE1" <-> "OE2" Residue "K ASP 876": "OD1" <-> "OD2" Residue "K ASP 880": "OD1" <-> "OD2" Residue "K ARG 881": "NH1" <-> "NH2" Residue "K ARG 926": "NH1" <-> "NH2" Residue "K GLU 1027": "OE1" <-> "OE2" Residue "K ARG 1051": "NH1" <-> "NH2" Residue "Q GLU 355": "OE1" <-> "OE2" Residue "Q ARG 382": "NH1" <-> "NH2" Residue "Q PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 420": "OD1" <-> "OD2" Residue "Q ASP 422": "OD1" <-> "OD2" Residue "Q PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 430": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19241 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1526 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain breaks: 2 Chain: "C" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1774 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4474 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 536} Chain breaks: 3 Chain: "E" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3441 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 19, 'TRANS': 413} Chain breaks: 3 Chain: "F" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 902 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 1 Chain: "G" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1108 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "H" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1803 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 2 Chain: "I" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 865 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "K" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2258 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain breaks: 3 Chain: "Q" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 7, 'TRANS': 76} Chain: "U" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 415 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain breaks: 2 Time building chain proxies: 9.25, per 1000 atoms: 0.48 Number of scatterers: 19241 At special positions: 0 Unit cell: (106.05, 148.05, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3666 8.00 N 3341 7.00 C 12168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.86 Conformation dependent library (CDL) restraints added in 3.4 seconds 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4652 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 13 sheets defined 50.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.549A pdb=" N THR B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.810A pdb=" N TYR B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.678A pdb=" N ALA B 344 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 345' Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.782A pdb=" N VAL C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 19 " --> pdb=" O MET C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 55 removed outlier: 3.552A pdb=" N THR C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 removed outlier: 4.009A pdb=" N VAL C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 65 " --> pdb=" O PRO C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 71 through 82 Processing helix chain 'C' and resid 192 through 202 removed outlier: 3.763A pdb=" N CYS C 199 " --> pdb=" O HIS C 195 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 200 " --> pdb=" O TRP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.937A pdb=" N ASP C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.162A pdb=" N LEU C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'C' and resid 229 through 264 removed outlier: 4.002A pdb=" N THR C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 320 through 324 removed outlier: 3.828A pdb=" N ASN C 324 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 71 Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.590A pdb=" N THR D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 3.591A pdb=" N ALA D 155 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 190 removed outlier: 3.777A pdb=" N LEU D 174 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.534A pdb=" N ASP D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.522A pdb=" N ILE D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 229' Processing helix chain 'D' and resid 231 through 240 removed outlier: 3.945A pdb=" N GLN D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 265 through 276 removed outlier: 3.524A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'E' and resid 17 through 25 removed outlier: 3.778A pdb=" N SER E 23 " --> pdb=" O ASP E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 59 removed outlier: 3.853A pdb=" N GLN E 51 " --> pdb=" O GLU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 removed outlier: 3.615A pdb=" N VAL E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 76 removed outlier: 4.078A pdb=" N ARG E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 76' Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.522A pdb=" N ASN E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 232 Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.575A pdb=" N ILE E 269 " --> pdb=" O VAL E 265 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE E 271 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN E 275 " --> pdb=" O PHE E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 305 through 309 removed outlier: 3.787A pdb=" N ILE E 308 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS E 309 " --> pdb=" O PRO E 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 305 through 309' Processing helix chain 'E' and resid 311 through 320 removed outlier: 3.584A pdb=" N ILE E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 320 " --> pdb=" O LEU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 361 removed outlier: 4.018A pdb=" N LEU E 346 " --> pdb=" O ARG E 342 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR E 356 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS E 359 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE E 361 " --> pdb=" O VAL E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.570A pdb=" N TYR E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 408 through 411 removed outlier: 4.313A pdb=" N ASN E 411 " --> pdb=" O PHE E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 429 through 433 removed outlier: 4.037A pdb=" N HIS E 433 " --> pdb=" O ILE E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 460 removed outlier: 3.766A pdb=" N ILE E 458 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 460 " --> pdb=" O THR E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 464 Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 50 through 78 removed outlier: 4.353A pdb=" N LEU F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA F 78 " --> pdb=" O TYR F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 89 through 101 removed outlier: 3.682A pdb=" N ILE G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 135 removed outlier: 3.643A pdb=" N LYS G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 145 removed outlier: 3.581A pdb=" N VAL G 140 " --> pdb=" O SER G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.719A pdb=" N GLN G 152 " --> pdb=" O ALA G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.765A pdb=" N GLN G 172 " --> pdb=" O GLN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 194 removed outlier: 4.619A pdb=" N SER G 190 " --> pdb=" O ASN G 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.577A pdb=" N LEU H 188 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 199 Processing helix chain 'H' and resid 211 through 221 Processing helix chain 'H' and resid 229 through 239 removed outlier: 3.765A pdb=" N ASN H 239 " --> pdb=" O ARG H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 256 removed outlier: 3.860A pdb=" N TRP H 247 " --> pdb=" O THR H 243 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN H 249 " --> pdb=" O LEU H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 264 removed outlier: 3.781A pdb=" N SER H 263 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 259 through 264' Processing helix chain 'H' and resid 268 through 284 Processing helix chain 'H' and resid 292 through 317 removed outlier: 4.914A pdb=" N THR H 315 " --> pdb=" O PHE H 311 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL H 316 " --> pdb=" O THR H 312 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG H 317 " --> pdb=" O ILE H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 349 removed outlier: 4.073A pdb=" N ARG H 346 " --> pdb=" O ALA H 342 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP H 347 " --> pdb=" O ALA H 343 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS H 349 " --> pdb=" O LYS H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 353 removed outlier: 3.844A pdb=" N LEU H 353 " --> pdb=" O ILE H 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 350 through 353' Processing helix chain 'H' and resid 356 through 365 Processing helix chain 'H' and resid 407 through 418 removed outlier: 3.688A pdb=" N ILE H 412 " --> pdb=" O THR H 408 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR H 413 " --> pdb=" O ASN H 409 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER H 417 " --> pdb=" O TYR H 413 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 428 Processing helix chain 'I' and resid 439 through 468 removed outlier: 3.919A pdb=" N THR I 455 " --> pdb=" O ASP I 451 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE I 460 " --> pdb=" O ASN I 456 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG I 463 " --> pdb=" O ALA I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 485 removed outlier: 4.108A pdb=" N ILE I 478 " --> pdb=" O GLU I 474 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN I 485 " --> pdb=" O HIS I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 524 removed outlier: 3.542A pdb=" N ASN I 511 " --> pdb=" O SER I 507 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 163 Processing helix chain 'K' and resid 167 through 185 Processing helix chain 'K' and resid 731 through 741 removed outlier: 3.559A pdb=" N SER K 735 " --> pdb=" O ASP K 731 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP K 737 " --> pdb=" O GLU K 733 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR K 741 " --> pdb=" O TRP K 737 " (cutoff:3.500A) Processing helix chain 'K' and resid 743 through 753 removed outlier: 3.513A pdb=" N GLU K 747 " --> pdb=" O LYS K 743 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR K 753 " --> pdb=" O CYS K 749 " (cutoff:3.500A) Processing helix chain 'K' and resid 868 through 884 removed outlier: 3.598A pdb=" N ASP K 872 " --> pdb=" O THR K 868 " (cutoff:3.500A) Processing helix chain 'K' and resid 901 through 916 Processing helix chain 'K' and resid 917 through 929 Processing helix chain 'K' and resid 975 through 989 removed outlier: 3.679A pdb=" N ILE K 979 " --> pdb=" O ASN K 975 " (cutoff:3.500A) Processing helix chain 'K' and resid 1000 through 1027 removed outlier: 3.707A pdb=" N ILE K1004 " --> pdb=" O HIS K1000 " (cutoff:3.500A) Processing helix chain 'K' and resid 1035 through 1046 removed outlier: 3.763A pdb=" N LEU K1040 " --> pdb=" O ASN K1036 " (cutoff:3.500A) Processing helix chain 'K' and resid 1053 through 1064 Processing helix chain 'K' and resid 1065 through 1085 Processing helix chain 'Q' and resid 354 through 366 Processing helix chain 'Q' and resid 381 through 398 removed outlier: 3.917A pdb=" N PHE Q 398 " --> pdb=" O PHE Q 394 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 29 removed outlier: 3.656A pdb=" N ALA U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA U 29 " --> pdb=" O ALA U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 113 Processing helix chain 'U' and resid 125 through 137 removed outlier: 3.759A pdb=" N ALA U 137 " --> pdb=" O ALA U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 152 removed outlier: 3.850A pdb=" N ALA U 145 " --> pdb=" O ALA U 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.817A pdb=" N LEU B 211 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 349 through 350 removed outlier: 3.691A pdb=" N HIS B 349 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.428A pdb=" N TYR D 242 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN D 280 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 244 " --> pdb=" O ASN D 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 781 through 784 removed outlier: 5.937A pdb=" N SER D 456 " --> pdb=" O ALA D 790 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA D 792 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N CYS D 458 " --> pdb=" O ALA D 792 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY D 794 " --> pdb=" O CYS D 458 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR D 460 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 469 through 474 removed outlier: 4.834A pdb=" N GLY D 484 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU D 472 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA D 482 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE D 474 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE D 480 " --> pdb=" O PHE D 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 528 through 533 removed outlier: 6.456A pdb=" N VAL D 549 " --> pdb=" O SER D 562 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER D 562 " --> pdb=" O VAL D 549 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 551 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 570 through 574 removed outlier: 6.451A pdb=" N ALA D 585 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL D 573 " --> pdb=" O ALA D 583 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA D 583 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER D 586 " --> pdb=" O THR D 590 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR D 590 " --> pdb=" O SER D 586 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER D 595 " --> pdb=" O PRO D 601 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 612 through 617 removed outlier: 3.832A pdb=" N THR D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS D 633 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU D 646 " --> pdb=" O CYS D 633 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET D 635 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 654 through 659 removed outlier: 3.626A pdb=" N LYS D 687 " --> pdb=" O VAL D 677 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP D 679 " --> pdb=" O ARG D 685 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG D 685 " --> pdb=" O ASP D 679 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 701 through 702 removed outlier: 3.924A pdb=" N ALA D 770 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP D 722 " --> pdb=" O LEU D 768 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU D 768 " --> pdb=" O ASP D 722 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AB3, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AB4, first strand: chain 'H' and resid 335 through 337 removed outlier: 6.561A pdb=" N TYR H 335 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 819 hydrogen bonds defined for protein. 2415 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: 5.74 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6241 1.34 - 1.46: 3683 1.46 - 1.58: 9563 1.58 - 1.70: 1 1.70 - 1.82: 109 Bond restraints: 19597 Sorted by residual: bond pdb=" C PRO E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.334 1.359 -0.025 8.40e-03 1.42e+04 9.11e+00 bond pdb=" C ASN D 123 " pdb=" N PRO D 124 " ideal model delta sigma weight residual 1.326 1.362 -0.035 1.44e-02 4.82e+03 6.06e+00 bond pdb=" C TYR D 600 " pdb=" N PRO D 601 " ideal model delta sigma weight residual 1.331 1.358 -0.026 1.21e-02 6.83e+03 4.78e+00 bond pdb=" C LYS E 204 " pdb=" N PRO E 205 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.87e+00 bond pdb=" CA THR K 953 " pdb=" CB THR K 953 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.69e-02 3.50e+03 2.94e+00 ... (remaining 19592 not shown) Histogram of bond angle deviations from ideal: 99.91 - 107.15: 582 107.15 - 114.39: 11445 114.39 - 121.63: 10080 121.63 - 128.87: 4273 128.87 - 136.11: 139 Bond angle restraints: 26519 Sorted by residual: angle pdb=" C ASN H 239 " pdb=" N ASN H 240 " pdb=" CA ASN H 240 " ideal model delta sigma weight residual 122.61 131.69 -9.08 1.56e+00 4.11e-01 3.39e+01 angle pdb=" C ASN D 504 " pdb=" N ILE D 505 " pdb=" CA ILE D 505 " ideal model delta sigma weight residual 121.97 132.17 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" CA LYS D 775 " pdb=" CB LYS D 775 " pdb=" CG LYS D 775 " ideal model delta sigma weight residual 114.10 125.11 -11.01 2.00e+00 2.50e-01 3.03e+01 angle pdb=" C ASP D 476 " pdb=" N ASP D 477 " pdb=" CA ASP D 477 " ideal model delta sigma weight residual 125.66 135.19 -9.53 1.85e+00 2.92e-01 2.65e+01 angle pdb=" C ARG H 403 " pdb=" N THR H 404 " pdb=" CA THR H 404 " ideal model delta sigma weight residual 122.08 129.35 -7.27 1.47e+00 4.63e-01 2.44e+01 ... (remaining 26514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 10537 17.89 - 35.77: 1154 35.77 - 53.66: 195 53.66 - 71.54: 43 71.54 - 89.43: 22 Dihedral angle restraints: 11951 sinusoidal: 4814 harmonic: 7137 Sorted by residual: dihedral pdb=" CA ASN D 504 " pdb=" C ASN D 504 " pdb=" N ILE D 505 " pdb=" CA ILE D 505 " ideal model delta harmonic sigma weight residual -180.00 -139.36 -40.64 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA ASP D 476 " pdb=" C ASP D 476 " pdb=" N ASP D 477 " pdb=" CA ASP D 477 " ideal model delta harmonic sigma weight residual -180.00 -148.32 -31.68 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA ASP D 546 " pdb=" C ASP D 546 " pdb=" N LYS D 547 " pdb=" CA LYS D 547 " ideal model delta harmonic sigma weight residual 180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 11948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2745 0.092 - 0.185: 255 0.185 - 0.277: 11 0.277 - 0.369: 2 0.369 - 0.462: 1 Chirality restraints: 3014 Sorted by residual: chirality pdb=" CB ILE H 350 " pdb=" CA ILE H 350 " pdb=" CG1 ILE H 350 " pdb=" CG2 ILE H 350 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CB VAL E 265 " pdb=" CA VAL E 265 " pdb=" CG1 VAL E 265 " pdb=" CG2 VAL E 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE C 21 " pdb=" CA ILE C 21 " pdb=" CG1 ILE C 21 " pdb=" CG2 ILE C 21 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3011 not shown) Planarity restraints: 3411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 243 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO H 244 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO H 244 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 244 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 775 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C LYS D 775 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS D 775 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS D 776 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 568 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO D 569 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 569 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 569 " -0.038 5.00e-02 4.00e+02 ... (remaining 3408 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3997 2.78 - 3.31: 17481 3.31 - 3.84: 31777 3.84 - 4.37: 36874 4.37 - 4.90: 63455 Nonbonded interactions: 153584 Sorted by model distance: nonbonded pdb=" OH TYR D 256 " pdb=" OG SER D 441 " model vdw 2.247 2.440 nonbonded pdb=" OG1 THR E 16 " pdb=" OD2 ASP F 32 " model vdw 2.281 2.440 nonbonded pdb=" OG1 THR K1042 " pdb=" OE2 GLU K1046 " model vdw 2.288 2.440 nonbonded pdb=" O SER D 656 " pdb=" OG1 THR D 668 " model vdw 2.288 2.440 nonbonded pdb=" O LEU Q 373 " pdb=" OH TYR Q 427 " model vdw 2.295 2.440 ... (remaining 153579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 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: 13.590 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 47.790 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.005 0.070 19597 Z= 0.299 Angle : 0.921 12.595 26519 Z= 0.506 Chirality : 0.055 0.462 3014 Planarity : 0.007 0.084 3411 Dihedral : 15.565 89.429 7299 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 0.43 % Allowed : 8.14 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -4.36 (0.13), residues: 2366 helix: -2.69 (0.11), residues: 1137 sheet: -1.55 (0.35), residues: 186 loop : -3.33 (0.15), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 486 HIS 0.013 0.001 HIS D 524 PHE 0.030 0.002 PHE D 582 TYR 0.033 0.002 TYR B 130 ARG 0.005 0.000 ARG H 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 367 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 307 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7771 (mm-30) REVERT: D 704 LYS cc_start: 0.7762 (tmtt) cc_final: 0.7153 (mmmt) REVERT: E 216 LYS cc_start: 0.1935 (mttp) cc_final: 0.1546 (mtmt) REVERT: E 348 ASP cc_start: 0.7099 (m-30) cc_final: 0.6406 (m-30) REVERT: H 186 MET cc_start: 0.6920 (tpp) cc_final: 0.6394 (tpp) REVERT: H 364 ASP cc_start: 0.6691 (m-30) cc_final: 0.6376 (m-30) REVERT: I 418 ARG cc_start: 0.7023 (ptt90) cc_final: 0.6708 (ptt-90) REVERT: I 422 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5955 (mm-30) REVERT: I 476 ARG cc_start: 0.6689 (ptm160) cc_final: 0.6317 (ptp-170) REVERT: I 481 HIS cc_start: 0.8109 (t70) cc_final: 0.7791 (t-170) REVERT: I 497 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5706 (mt-10) REVERT: K 1039 MET cc_start: 0.7901 (mtm) cc_final: 0.7654 (mtp) REVERT: Q 409 TYR cc_start: 0.5755 (t80) cc_final: 0.5551 (t80) outliers start: 9 outliers final: 2 residues processed: 373 average time/residue: 0.3603 time to fit residues: 196.1320 Evaluate side-chains 243 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 216 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 336 HIS C 13 GLN C 209 ASN C 227 HIS C 319 HIS D 274 ASN D 275 GLN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 GLN D 463 GLN D 486 GLN ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 HIS D 618 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN E 127 GLN E 217 HIS F 51 GLN G 118 GLN ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN H 219 ASN H 240 ASN H 303 GLN H 373 ASN I 472 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 505 ASN ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 856 ASN K 890 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19597 Z= 0.192 Angle : 0.614 9.117 26519 Z= 0.321 Chirality : 0.042 0.176 3014 Planarity : 0.005 0.063 3411 Dihedral : 5.920 50.664 2620 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer: Outliers : 2.18 % Allowed : 14.77 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.64 (0.15), residues: 2366 helix: -0.82 (0.14), residues: 1156 sheet: -1.05 (0.38), residues: 176 loop : -3.01 (0.16), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 247 HIS 0.005 0.001 HIS K 920 PHE 0.016 0.001 PHE C 236 TYR 0.022 0.001 TYR D 184 ARG 0.006 0.000 ARG D 760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 284 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7497 (pp) REVERT: D 704 LYS cc_start: 0.7816 (tmtt) cc_final: 0.7229 (mmmt) REVERT: E 216 LYS cc_start: 0.2121 (mttp) cc_final: 0.1648 (mtmt) REVERT: E 348 ASP cc_start: 0.7225 (m-30) cc_final: 0.6559 (m-30) REVERT: E 407 PHE cc_start: 0.7924 (t80) cc_final: 0.7513 (t80) REVERT: H 336 LYS cc_start: 0.6534 (pttt) cc_final: 0.6299 (pttm) REVERT: H 364 ASP cc_start: 0.7142 (m-30) cc_final: 0.6663 (m-30) REVERT: I 418 ARG cc_start: 0.7015 (ptt90) cc_final: 0.6693 (ptt-90) REVERT: I 433 ASP cc_start: 0.8052 (t0) cc_final: 0.7771 (t0) REVERT: I 476 ARG cc_start: 0.6739 (ptm160) cc_final: 0.6422 (ptp-170) REVERT: I 497 GLU cc_start: 0.6186 (mt-10) cc_final: 0.5711 (mt-10) REVERT: K 856 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.7013 (m-40) REVERT: K 1039 MET cc_start: 0.7918 (mtm) cc_final: 0.7671 (mtp) outliers start: 46 outliers final: 25 residues processed: 312 average time/residue: 0.3295 time to fit residues: 155.2553 Evaluate side-chains 274 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 247 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 147 optimal weight: 0.0470 chunk 59 optimal weight: 8.9990 chunk 216 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 192 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN F 61 HIS H 283 HIS ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1025 HIS ** Q 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 19597 Z= 0.274 Angle : 0.631 8.216 26519 Z= 0.330 Chirality : 0.044 0.210 3014 Planarity : 0.005 0.058 3411 Dihedral : 5.830 54.956 2619 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 3.22 % Allowed : 16.81 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.04 (0.16), residues: 2366 helix: -0.19 (0.15), residues: 1155 sheet: -1.12 (0.38), residues: 178 loop : -2.81 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 247 HIS 0.005 0.001 HIS E 217 PHE 0.017 0.002 PHE C 236 TYR 0.024 0.002 TYR D 581 ARG 0.006 0.000 ARG K 745 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 254 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7540 (pp) REVERT: C 42 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6719 (mm-30) REVERT: D 472 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6753 (pt) REVERT: D 704 LYS cc_start: 0.7940 (tmtt) cc_final: 0.7326 (mmmt) REVERT: E 216 LYS cc_start: 0.2236 (mttp) cc_final: 0.1713 (mtmt) REVERT: E 407 PHE cc_start: 0.7924 (t80) cc_final: 0.7481 (t80) REVERT: I 418 ARG cc_start: 0.7183 (ptt90) cc_final: 0.6681 (ptt-90) REVERT: I 476 ARG cc_start: 0.6770 (ptm160) cc_final: 0.6530 (ptp-170) REVERT: I 497 GLU cc_start: 0.6301 (mt-10) cc_final: 0.5886 (mt-10) REVERT: K 1039 MET cc_start: 0.8067 (mtm) cc_final: 0.7842 (mtp) outliers start: 68 outliers final: 49 residues processed: 297 average time/residue: 0.3197 time to fit residues: 144.8031 Evaluate side-chains 288 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 237 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 357 LYS Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 217 optimal weight: 0.0670 chunk 230 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN H 240 ASN ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19597 Z= 0.196 Angle : 0.578 8.015 26519 Z= 0.302 Chirality : 0.042 0.199 3014 Planarity : 0.004 0.057 3411 Dihedral : 5.535 55.623 2619 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.55 % Favored : 93.41 % Rotamer: Outliers : 3.46 % Allowed : 18.28 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.57 (0.17), residues: 2366 helix: 0.26 (0.15), residues: 1158 sheet: -1.02 (0.38), residues: 178 loop : -2.63 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 196 HIS 0.004 0.001 HIS E 217 PHE 0.019 0.001 PHE C 236 TYR 0.015 0.001 TYR D 581 ARG 0.003 0.000 ARG D 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 263 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7539 (pp) REVERT: C 42 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6706 (mm-30) REVERT: C 307 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7643 (mm-30) REVERT: D 167 LEU cc_start: 0.3749 (OUTLIER) cc_final: 0.3417 (tt) REVERT: D 472 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6712 (pt) REVERT: D 704 LYS cc_start: 0.7941 (tmtt) cc_final: 0.7374 (mmmt) REVERT: D 715 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8337 (p0) REVERT: E 407 PHE cc_start: 0.7906 (t80) cc_final: 0.7438 (t80) REVERT: H 198 MET cc_start: 0.8343 (mtp) cc_final: 0.8122 (mtt) REVERT: H 336 LYS cc_start: 0.6586 (pttt) cc_final: 0.6278 (pttm) REVERT: H 361 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: I 418 ARG cc_start: 0.7125 (ptt90) cc_final: 0.6733 (ptt-90) REVERT: I 476 ARG cc_start: 0.6742 (ptm160) cc_final: 0.6516 (ptp-170) REVERT: I 497 GLU cc_start: 0.6184 (mt-10) cc_final: 0.5791 (mt-10) REVERT: K 927 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6681 (mpp) REVERT: K 1039 MET cc_start: 0.8042 (mtm) cc_final: 0.7809 (mtp) outliers start: 73 outliers final: 52 residues processed: 315 average time/residue: 0.3226 time to fit residues: 154.1397 Evaluate side-chains 300 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 242 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 927 MET Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 171 optimal weight: 0.2980 chunk 94 optimal weight: 0.0270 chunk 196 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN C 152 HIS C 209 ASN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 914 GLN ** Q 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 19597 Z= 0.179 Angle : 0.569 8.011 26519 Z= 0.296 Chirality : 0.042 0.161 3014 Planarity : 0.004 0.063 3411 Dihedral : 5.284 43.616 2619 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.72 % Favored : 93.24 % Rotamer: Outliers : 3.88 % Allowed : 19.13 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.28 (0.17), residues: 2366 helix: 0.50 (0.15), residues: 1167 sheet: -0.90 (0.38), residues: 177 loop : -2.52 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 678 HIS 0.004 0.001 HIS E 217 PHE 0.025 0.001 PHE D 186 TYR 0.022 0.001 TYR D 179 ARG 0.006 0.000 ARG D 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 257 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7529 (pp) REVERT: C 42 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6716 (mm-30) REVERT: C 233 ILE cc_start: 0.8094 (mm) cc_final: 0.7744 (tp) REVERT: C 307 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7659 (mm-30) REVERT: D 689 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.6730 (mmt) REVERT: D 704 LYS cc_start: 0.7842 (tmtt) cc_final: 0.7364 (mmmt) REVERT: D 715 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8331 (p0) REVERT: E 407 PHE cc_start: 0.7927 (t80) cc_final: 0.7481 (t80) REVERT: H 347 ASP cc_start: 0.8148 (p0) cc_final: 0.7837 (p0) REVERT: H 361 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: I 418 ARG cc_start: 0.7150 (ptt90) cc_final: 0.6741 (ptt-90) REVERT: I 476 ARG cc_start: 0.6721 (ptm160) cc_final: 0.6496 (ptp-170) REVERT: I 497 GLU cc_start: 0.6164 (mt-10) cc_final: 0.5759 (mt-10) REVERT: K 927 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6579 (mpp) REVERT: K 1039 MET cc_start: 0.8047 (mtm) cc_final: 0.7814 (mtp) outliers start: 82 outliers final: 55 residues processed: 310 average time/residue: 0.3406 time to fit residues: 163.6439 Evaluate side-chains 299 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 239 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 357 LYS Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 927 MET Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 961 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN H 240 ASN K 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 19597 Z= 0.169 Angle : 0.570 9.074 26519 Z= 0.294 Chirality : 0.042 0.184 3014 Planarity : 0.004 0.063 3411 Dihedral : 5.069 41.332 2619 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.26 % Favored : 93.70 % Rotamer: Outliers : 3.93 % Allowed : 19.74 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.04 (0.17), residues: 2366 helix: 0.70 (0.16), residues: 1167 sheet: -0.68 (0.39), residues: 171 loop : -2.42 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 737 HIS 0.004 0.001 HIS I 481 PHE 0.028 0.001 PHE D 186 TYR 0.024 0.001 TYR D 179 ARG 0.005 0.000 ARG F 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 251 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7525 (pp) REVERT: C 42 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6727 (mm-30) REVERT: C 307 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 689 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.6690 (mmt) REVERT: D 704 LYS cc_start: 0.7823 (tmtt) cc_final: 0.7352 (mmmt) REVERT: D 715 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8330 (p0) REVERT: D 777 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.7955 (p) REVERT: E 407 PHE cc_start: 0.7797 (t80) cc_final: 0.7329 (t80) REVERT: H 250 ASP cc_start: 0.7039 (t0) cc_final: 0.6751 (t0) REVERT: H 347 ASP cc_start: 0.8083 (p0) cc_final: 0.7798 (p0) REVERT: H 361 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7827 (mm-30) REVERT: H 413 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: I 418 ARG cc_start: 0.7145 (ptt90) cc_final: 0.6729 (ptt-90) REVERT: I 497 GLU cc_start: 0.6053 (mt-10) cc_final: 0.5690 (mt-10) REVERT: K 927 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6580 (mpp) REVERT: K 1039 MET cc_start: 0.8035 (mtm) cc_final: 0.7809 (mtp) outliers start: 83 outliers final: 62 residues processed: 306 average time/residue: 0.3170 time to fit residues: 149.4989 Evaluate side-chains 313 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 244 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 357 LYS Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 413 TYR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 927 MET Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 131 optimal weight: 4.9990 chunk 168 optimal weight: 0.0770 chunk 130 optimal weight: 0.6980 chunk 193 optimal weight: 0.2980 chunk 128 optimal weight: 0.3980 chunk 229 optimal weight: 0.3980 chunk 143 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 0.0970 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 GLN K1036 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 19597 Z= 0.144 Angle : 0.553 7.850 26519 Z= 0.286 Chirality : 0.041 0.170 3014 Planarity : 0.004 0.061 3411 Dihedral : 4.828 38.128 2619 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.00 % Favored : 93.96 % Rotamer: Outliers : 2.94 % Allowed : 20.98 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2366 helix: 0.91 (0.16), residues: 1165 sheet: -0.49 (0.41), residues: 152 loop : -2.33 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 737 HIS 0.005 0.001 HIS B 359 PHE 0.030 0.001 PHE D 186 TYR 0.025 0.001 TYR D 179 ARG 0.006 0.000 ARG Q 415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 256 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7526 (pp) REVERT: D 689 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.6669 (mmt) REVERT: D 704 LYS cc_start: 0.7768 (tmtt) cc_final: 0.7345 (mmmt) REVERT: D 715 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8418 (p0) REVERT: D 751 GLN cc_start: 0.7024 (mm110) cc_final: 0.6649 (mm-40) REVERT: D 777 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7953 (p) REVERT: E 407 PHE cc_start: 0.7510 (t80) cc_final: 0.7067 (t80) REVERT: H 250 ASP cc_start: 0.7064 (t0) cc_final: 0.6776 (t0) REVERT: H 347 ASP cc_start: 0.8090 (p0) cc_final: 0.7828 (p0) REVERT: H 413 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6358 (m-80) REVERT: I 418 ARG cc_start: 0.7117 (ptt90) cc_final: 0.6721 (ptt-90) REVERT: K 747 GLU cc_start: 0.7623 (tp30) cc_final: 0.7300 (tp30) REVERT: K 927 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6584 (mpp) REVERT: K 1039 MET cc_start: 0.8005 (mtm) cc_final: 0.7745 (mtp) outliers start: 62 outliers final: 44 residues processed: 300 average time/residue: 0.3064 time to fit residues: 142.6716 Evaluate side-chains 294 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 244 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 311 PHE Chi-restraints excluded: chain H residue 357 LYS Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 413 TYR Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 927 MET Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 961 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 113 optimal weight: 0.0170 chunk 21 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN C 209 ASN ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN H 240 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 19597 Z= 0.174 Angle : 0.566 7.659 26519 Z= 0.292 Chirality : 0.042 0.173 3014 Planarity : 0.004 0.068 3411 Dihedral : 4.803 37.133 2619 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.34 % Favored : 93.62 % Rotamer: Outliers : 3.36 % Allowed : 21.07 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2366 helix: 0.98 (0.16), residues: 1166 sheet: -0.46 (0.41), residues: 154 loop : -2.34 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 737 HIS 0.005 0.001 HIS B 359 PHE 0.031 0.001 PHE D 186 TYR 0.026 0.001 TYR D 179 ARG 0.006 0.000 ARG Q 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 244 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 MET cc_start: 0.8104 (mmm) cc_final: 0.7837 (mmm) REVERT: B 327 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7548 (pp) REVERT: C 14 MET cc_start: 0.7849 (mtm) cc_final: 0.7391 (mtm) REVERT: C 42 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6474 (mm-30) REVERT: C 307 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 689 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.6716 (mmt) REVERT: D 704 LYS cc_start: 0.7793 (tmtt) cc_final: 0.7372 (mmmt) REVERT: D 715 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8444 (p0) REVERT: D 751 GLN cc_start: 0.7083 (mm110) cc_final: 0.6733 (mm-40) REVERT: D 777 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7939 (p) REVERT: E 407 PHE cc_start: 0.7572 (t80) cc_final: 0.7148 (t80) REVERT: G 81 MET cc_start: 0.7436 (ttm) cc_final: 0.6838 (ttm) REVERT: H 250 ASP cc_start: 0.7117 (t0) cc_final: 0.6826 (t0) REVERT: H 347 ASP cc_start: 0.8096 (p0) cc_final: 0.7850 (p0) REVERT: H 361 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: H 413 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: I 418 ARG cc_start: 0.7143 (ptt90) cc_final: 0.6736 (ptt-90) REVERT: I 497 GLU cc_start: 0.6209 (mt-10) cc_final: 0.5998 (mt-10) REVERT: K 927 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6604 (mpp) REVERT: K 1039 MET cc_start: 0.8025 (mtm) cc_final: 0.7785 (mtp) outliers start: 71 outliers final: 56 residues processed: 293 average time/residue: 0.2993 time to fit residues: 135.5428 Evaluate side-chains 300 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 237 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 311 PHE Chi-restraints excluded: chain H residue 357 LYS Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 413 TYR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 901 LEU Chi-restraints excluded: chain K residue 927 MET Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 202 optimal weight: 0.3980 chunk 140 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** D 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 19597 Z= 0.197 Angle : 0.576 8.029 26519 Z= 0.297 Chirality : 0.042 0.214 3014 Planarity : 0.004 0.066 3411 Dihedral : 4.789 36.939 2617 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 3.46 % Allowed : 21.12 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2366 helix: 0.97 (0.16), residues: 1166 sheet: -0.45 (0.40), residues: 164 loop : -2.34 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 737 HIS 0.005 0.001 HIS B 359 PHE 0.032 0.001 PHE D 186 TYR 0.027 0.001 TYR D 179 ARG 0.006 0.000 ARG Q 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 246 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 MET cc_start: 0.8111 (mmm) cc_final: 0.7840 (mmm) REVERT: B 327 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7539 (pp) REVERT: C 42 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6510 (mm-30) REVERT: D 689 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.6759 (mmt) REVERT: D 704 LYS cc_start: 0.7820 (tmtt) cc_final: 0.7382 (mmmt) REVERT: D 715 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8312 (p0) REVERT: D 751 GLN cc_start: 0.7059 (mm110) cc_final: 0.6721 (mm-40) REVERT: D 777 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7968 (p) REVERT: E 407 PHE cc_start: 0.7608 (t80) cc_final: 0.7136 (t80) REVERT: H 250 ASP cc_start: 0.7209 (t0) cc_final: 0.6961 (t0) REVERT: H 347 ASP cc_start: 0.8057 (p0) cc_final: 0.7824 (p0) REVERT: H 361 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7808 (mm-30) REVERT: H 413 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6608 (m-80) REVERT: I 418 ARG cc_start: 0.7134 (ptt90) cc_final: 0.6727 (ptt-90) REVERT: I 476 ARG cc_start: 0.7030 (ptp-110) cc_final: 0.6733 (ptp-110) REVERT: I 497 GLU cc_start: 0.6162 (mt-10) cc_final: 0.5923 (mt-10) REVERT: K 927 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6613 (mpp) REVERT: K 1039 MET cc_start: 0.8016 (mtm) cc_final: 0.7772 (mtp) outliers start: 73 outliers final: 59 residues processed: 299 average time/residue: 0.3332 time to fit residues: 156.1673 Evaluate side-chains 302 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 236 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 357 LYS Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 413 TYR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 901 LEU Chi-restraints excluded: chain K residue 927 MET Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain K residue 1040 LEU Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.0040 chunk 137 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 218 optimal weight: 0.6980 chunk 188 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** D 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS G 172 GLN H 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 19597 Z= 0.186 Angle : 0.574 8.545 26519 Z= 0.296 Chirality : 0.042 0.208 3014 Planarity : 0.004 0.073 3411 Dihedral : 4.771 36.307 2617 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 3.36 % Allowed : 21.73 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2366 helix: 1.00 (0.16), residues: 1165 sheet: -0.45 (0.40), residues: 164 loop : -2.32 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 737 HIS 0.004 0.001 HIS B 359 PHE 0.033 0.001 PHE D 186 TYR 0.028 0.001 TYR D 179 ARG 0.006 0.000 ARG Q 415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 236 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 MET cc_start: 0.8086 (mmm) cc_final: 0.7816 (mmm) REVERT: B 327 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7556 (pp) REVERT: C 42 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6477 (mm-30) REVERT: D 689 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.6756 (mmt) REVERT: D 704 LYS cc_start: 0.7816 (tmtt) cc_final: 0.7375 (mmmt) REVERT: D 715 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8313 (p0) REVERT: D 751 GLN cc_start: 0.6934 (mm110) cc_final: 0.6590 (mm-40) REVERT: D 777 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7961 (p) REVERT: E 407 PHE cc_start: 0.7682 (t80) cc_final: 0.7209 (t80) REVERT: H 250 ASP cc_start: 0.7185 (t0) cc_final: 0.6946 (t0) REVERT: H 347 ASP cc_start: 0.8131 (p0) cc_final: 0.7908 (p0) REVERT: H 413 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: I 418 ARG cc_start: 0.7124 (ptt90) cc_final: 0.6726 (ptt-90) REVERT: I 476 ARG cc_start: 0.7027 (ptp-110) cc_final: 0.6729 (ptp-110) REVERT: I 497 GLU cc_start: 0.6260 (mt-10) cc_final: 0.5999 (mt-10) REVERT: K 927 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6625 (mpp) REVERT: K 1039 MET cc_start: 0.8020 (mtm) cc_final: 0.7774 (mtp) outliers start: 71 outliers final: 61 residues processed: 287 average time/residue: 0.3178 time to fit residues: 140.8918 Evaluate side-chains 296 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 229 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 357 LYS Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 413 TYR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 901 LEU Chi-restraints excluded: chain K residue 927 MET Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain K residue 1040 LEU Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** D 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.152204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.125559 restraints weight = 30925.727| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.34 r_work: 0.3444 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 19597 Z= 0.252 Angle : 0.801 59.164 26519 Z= 0.466 Chirality : 0.045 0.599 3014 Planarity : 0.005 0.131 3411 Dihedral : 4.821 36.319 2617 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 3.31 % Allowed : 21.73 % Favored : 74.95 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.72 (0.17), residues: 2366 helix: 0.99 (0.16), residues: 1165 sheet: -0.45 (0.40), residues: 164 loop : -2.31 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 737 HIS 0.004 0.001 HIS B 359 PHE 0.029 0.001 PHE D 186 TYR 0.025 0.001 TYR D 179 ARG 0.006 0.000 ARG D 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4216.81 seconds wall clock time: 77 minutes 39.03 seconds (4659.03 seconds total)