Starting phenix.real_space_refine on Fri Feb 16 20:17:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/02_2024/6wul_21915.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/02_2024/6wul_21915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/02_2024/6wul_21915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/02_2024/6wul_21915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/02_2024/6wul_21915.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/02_2024/6wul_21915.pdb" } resolution = 3.2 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= 0.013 sd= 0.164 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 30 5.16 5 C 10400 2.51 5 N 2920 2.21 5 O 3036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "B ASP 63": "OD1" <-> "OD2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "C PHE -25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU -24": "OE1" <-> "OE2" Residue "C PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 309": "OD1" <-> "OD2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ASP 329": "OD1" <-> "OD2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E ASP 85": "OD1" <-> "OD2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 196": "OD1" <-> "OD2" Residue "E PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E ASP 394": "OD1" <-> "OD2" Residue "E PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 413": "OD1" <-> "OD2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 482": "NH1" <-> "NH2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "F PHE -25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU -24": "OE1" <-> "OE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 18": "OD1" <-> "OD2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F ASP 286": "OD1" <-> "OD2" Residue "F TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 309": "OD1" <-> "OD2" Residue "F PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 415": "OE1" <-> "OE2" 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: 16386 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2284 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 22, 'TRANS': 272} Chain breaks: 2 Chain: "B" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3295 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 3 Chain: "C" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2614 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain breaks: 3 Chain: "D" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2284 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 22, 'TRANS': 272} Chain breaks: 2 Chain: "E" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3295 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2614 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain breaks: 3 Time building chain proxies: 10.42, per 1000 atoms: 0.64 Number of scatterers: 16386 At special positions: 0 Unit cell: (119.78, 155.82, 112.36, 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 30 16.00 O 3036 8.00 N 2920 7.00 C 10400 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: 6.52 Conformation dependent library (CDL) restraints added in 3.4 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 38.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.921A pdb=" N ARG A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.439A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 150 through 162 removed outlier: 3.926A pdb=" N ALA A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.890A pdb=" N SER A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 192' Processing helix chain 'A' and resid 193 through 213 removed outlier: 4.331A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.879A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 286 removed outlier: 4.086A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'B' and resid 58 through 67 removed outlier: 3.619A pdb=" N LEU B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'C' and resid 18 through 32 removed outlier: 3.612A pdb=" N LEU C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 removed outlier: 4.039A pdb=" N VAL C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 106 through 121 removed outlier: 3.666A pdb=" N ALA C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.694A pdb=" N ALA C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.632A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 170 removed outlier: 3.600A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.830A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 284 removed outlier: 3.814A pdb=" N LEU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.574A pdb=" N CYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.546A pdb=" N GLY C 319 " --> pdb=" O PRO C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 354 through 378 Processing helix chain 'C' and resid 386 through 408 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.921A pdb=" N ARG D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 82 removed outlier: 4.440A pdb=" N TRP D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.926A pdb=" N ALA D 158 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 160 " --> pdb=" O TYR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 178 through 187 Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.891A pdb=" N SER D 191 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 193 through 213 removed outlier: 4.331A pdb=" N ALA D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.879A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 286 removed outlier: 4.087A pdb=" N TYR D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 308 Processing helix chain 'D' and resid 311 through 321 Processing helix chain 'E' and resid 58 through 67 removed outlier: 3.619A pdb=" N LEU E 62 " --> pdb=" O ARG E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 79 through 94 Processing helix chain 'E' and resid 255 through 261 Processing helix chain 'E' and resid 446 through 463 Processing helix chain 'F' and resid 18 through 32 removed outlier: 3.612A pdb=" N LEU F 22 " --> pdb=" O ASP F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 47 removed outlier: 4.040A pdb=" N VAL F 47 " --> pdb=" O PRO F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 73 Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.666A pdb=" N ALA F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 141 through 148 removed outlier: 3.694A pdb=" N ALA F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 156 removed outlier: 3.632A pdb=" N TRP F 156 " --> pdb=" O PRO F 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 153 through 156' Processing helix chain 'F' and resid 157 through 170 removed outlier: 3.600A pdb=" N ALA F 161 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 254 removed outlier: 3.831A pdb=" N VAL F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL F 252 " --> pdb=" O GLU F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 284 removed outlier: 3.813A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 300 Processing helix chain 'F' and resid 300 through 315 removed outlier: 3.575A pdb=" N CYS F 304 " --> pdb=" O TYR F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.546A pdb=" N GLY F 319 " --> pdb=" O PRO F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'F' and resid 354 through 378 Processing helix chain 'F' and resid 386 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90 removed outlier: 3.802A pdb=" N PHE A 103 " --> pdb=" O TYR A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 106 through 109 removed outlier: 6.236A pdb=" N THR B 48 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE B 130 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU B 50 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.565A pdb=" N SER B 188 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU B 197 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B 309 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 345 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 340 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 236 removed outlier: 4.566A pdb=" N PHE B 309 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 345 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 340 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 401 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 421 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 471 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 206 through 210 removed outlier: 3.766A pdb=" N GLU B 217 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS B 215 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 41 removed outlier: 7.103A pdb=" N ILE C 40 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU C 5 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 54 " --> pdb=" O HIS C 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 87 through 90 removed outlier: 3.802A pdb=" N PHE D 103 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 106 through 109 removed outlier: 6.236A pdb=" N THR E 48 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE E 130 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU E 50 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 168 removed outlier: 3.565A pdb=" N SER E 188 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU E 197 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE E 309 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR E 345 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 314 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 339 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG E 340 " --> pdb=" O ALA E 398 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 235 through 236 removed outlier: 4.566A pdb=" N PHE E 309 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR E 345 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 314 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 339 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG E 340 " --> pdb=" O ALA E 398 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 401 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR E 421 " --> pdb=" O GLY E 471 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY E 471 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 206 through 210 removed outlier: 3.766A pdb=" N GLU E 217 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS E 215 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 319 through 320 Processing sheet with id=AB5, first strand: chain 'F' and resid 40 through 41 removed outlier: 7.103A pdb=" N ILE F 40 " --> pdb=" O VAL F 3 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU F 5 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR F 54 " --> pdb=" O HIS F 6 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2046 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: 5.24 Time building geometry restraints manager: 7.01 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: 5455 1.34 - 1.46: 3084 1.46 - 1.57: 8175 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 16764 Sorted by residual: bond pdb=" C ALA B 357 " pdb=" N GLN B 358 " ideal model delta sigma weight residual 1.331 1.299 0.032 2.07e-02 2.33e+03 2.43e+00 bond pdb=" C ALA E 357 " pdb=" N GLN E 358 " ideal model delta sigma weight residual 1.331 1.300 0.031 2.07e-02 2.33e+03 2.31e+00 bond pdb=" CG LEU E 250 " pdb=" CD2 LEU E 250 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.90e+00 bond pdb=" CG LEU B 250 " pdb=" CD2 LEU B 250 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" CA ALA B 207 " pdb=" C ALA B 207 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.08e-02 8.57e+03 1.74e+00 ... (remaining 16759 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 645 106.65 - 113.50: 9119 113.50 - 120.35: 6422 120.35 - 127.19: 6367 127.19 - 134.04: 255 Bond angle restraints: 22808 Sorted by residual: angle pdb=" C GLY B 193 " pdb=" N ASN B 194 " pdb=" CA ASN B 194 " ideal model delta sigma weight residual 121.61 130.04 -8.43 1.39e+00 5.18e-01 3.68e+01 angle pdb=" C GLY E 193 " pdb=" N ASN E 194 " pdb=" CA ASN E 194 " ideal model delta sigma weight residual 121.61 130.01 -8.40 1.39e+00 5.18e-01 3.65e+01 angle pdb=" N TYR D 32 " pdb=" CA TYR D 32 " pdb=" C TYR D 32 " ideal model delta sigma weight residual 110.44 116.86 -6.42 1.20e+00 6.94e-01 2.86e+01 angle pdb=" N TYR A 32 " pdb=" CA TYR A 32 " pdb=" C TYR A 32 " ideal model delta sigma weight residual 110.44 116.85 -6.41 1.20e+00 6.94e-01 2.85e+01 angle pdb=" N GLU D 258 " pdb=" CA GLU D 258 " pdb=" CB GLU D 258 " ideal model delta sigma weight residual 114.17 109.79 4.38 1.14e+00 7.69e-01 1.48e+01 ... (remaining 22803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 8724 16.73 - 33.46: 906 33.46 - 50.19: 226 50.19 - 66.92: 74 66.92 - 83.65: 22 Dihedral angle restraints: 9952 sinusoidal: 3810 harmonic: 6142 Sorted by residual: dihedral pdb=" CA PRO D 34 " pdb=" C PRO D 34 " pdb=" N ASN D 35 " pdb=" CA ASN D 35 " ideal model delta harmonic sigma weight residual -180.00 -148.99 -31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA PRO A 34 " pdb=" C PRO A 34 " pdb=" N ASN A 35 " pdb=" CA ASN A 35 " ideal model delta harmonic sigma weight residual -180.00 -149.06 -30.94 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ALA E 185 " pdb=" C ALA E 185 " pdb=" N THR E 186 " pdb=" CA THR E 186 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 9949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1650 0.037 - 0.074: 633 0.074 - 0.110: 211 0.110 - 0.147: 64 0.147 - 0.184: 6 Chirality restraints: 2564 Sorted by residual: chirality pdb=" CA LEU F 52 " pdb=" N LEU F 52 " pdb=" C LEU F 52 " pdb=" CB LEU F 52 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA THR E 186 " pdb=" N THR E 186 " pdb=" C THR E 186 " pdb=" CB THR E 186 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2561 not shown) Planarity restraints: 2962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 124 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO C 125 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 124 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO F 125 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 125 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 125 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 355 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C PRO F 355 " -0.035 2.00e-02 2.50e+03 pdb=" O PRO F 355 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU F 356 " 0.012 2.00e-02 2.50e+03 ... (remaining 2959 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 398 2.66 - 3.22: 14903 3.22 - 3.78: 23895 3.78 - 4.34: 32676 4.34 - 4.90: 55920 Nonbonded interactions: 127792 Sorted by model distance: nonbonded pdb=" O THR D 259 " pdb=" OG1 THR D 259 " model vdw 2.101 2.440 nonbonded pdb=" O THR A 259 " pdb=" OG1 THR A 259 " model vdw 2.101 2.440 nonbonded pdb=" OG SER D 41 " pdb=" OG1 THR E 257 " model vdw 2.174 2.440 nonbonded pdb=" OG1 THR A 57 " pdb=" OD2 ASP A 60 " model vdw 2.191 2.440 nonbonded pdb=" OG1 THR D 57 " pdb=" OD2 ASP D 60 " model vdw 2.191 2.440 ... (remaining 127787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 0.580 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: 3.770 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 47.720 Find NCS groups from input model: 0.850 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 0.046 16764 Z= 0.344 Angle : 0.829 8.435 22808 Z= 0.476 Chirality : 0.045 0.184 2564 Planarity : 0.005 0.051 2962 Dihedral : 15.562 83.654 6012 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.71 % Favored : 87.19 % Rotamer: Outliers : 7.00 % Allowed : 13.58 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.87 (0.16), residues: 2124 helix: -1.26 (0.17), residues: 764 sheet: -3.07 (0.23), residues: 388 loop : -3.46 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 360 HIS 0.004 0.001 HIS E 215 PHE 0.012 0.002 PHE E 396 TYR 0.010 0.001 TYR F 37 ARG 0.003 0.000 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 212 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 254 LEU cc_start: 0.8572 (tp) cc_final: 0.8256 (tp) REVERT: A 304 MET cc_start: 0.8231 (mtp) cc_final: 0.7945 (mtm) REVERT: B 99 ILE cc_start: 0.7577 (mt) cc_final: 0.7162 (mt) REVERT: B 137 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6764 (tmm160) REVERT: B 202 GLU cc_start: 0.7748 (tt0) cc_final: 0.7491 (tt0) REVERT: B 358 GLN cc_start: 0.8518 (mt0) cc_final: 0.8070 (mm-40) REVERT: B 467 SER cc_start: 0.7206 (OUTLIER) cc_final: 0.6944 (m) REVERT: B 485 LEU cc_start: 0.8026 (tt) cc_final: 0.7693 (mm) REVERT: C 247 ARG cc_start: 0.7274 (mtp85) cc_final: 0.6859 (ttt-90) REVERT: C 251 ASP cc_start: 0.7885 (m-30) cc_final: 0.7175 (m-30) REVERT: D 261 TRP cc_start: 0.8165 (m100) cc_final: 0.7880 (m100) REVERT: E 108 PHE cc_start: 0.7647 (m-80) cc_final: 0.7048 (m-10) REVERT: E 137 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6497 (tmm160) REVERT: E 202 GLU cc_start: 0.7781 (tt0) cc_final: 0.7544 (tt0) REVERT: E 358 GLN cc_start: 0.8505 (mt0) cc_final: 0.8076 (mm-40) REVERT: E 375 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7559 (mtm180) REVERT: E 467 SER cc_start: 0.7362 (OUTLIER) cc_final: 0.7068 (m) REVERT: F 247 ARG cc_start: 0.7250 (mtp85) cc_final: 0.6912 (ttt-90) REVERT: F 251 ASP cc_start: 0.7839 (m-30) cc_final: 0.7131 (m-30) outliers start: 118 outliers final: 75 residues processed: 323 average time/residue: 0.3569 time to fit residues: 160.0495 Evaluate side-chains 251 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 172 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 472 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 202 HIS A 211 GLN A 310 ASN B 148 ASN B 286 GLN B 385 HIS B 431 ASN C 30 GLN C 330 GLN D 69 ASN D 310 ASN E 148 ASN E 286 GLN E 385 HIS E 431 ASN F 30 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16764 Z= 0.240 Angle : 0.685 9.069 22808 Z= 0.344 Chirality : 0.044 0.161 2564 Planarity : 0.005 0.046 2962 Dihedral : 9.068 56.811 2475 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.68 % Favored : 88.23 % Rotamer: Outliers : 6.82 % Allowed : 16.01 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.66 (0.18), residues: 2124 helix: 0.05 (0.19), residues: 754 sheet: -2.48 (0.24), residues: 392 loop : -2.98 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 360 HIS 0.007 0.001 HIS A 144 PHE 0.020 0.001 PHE D 262 TYR 0.013 0.001 TYR A 32 ARG 0.005 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 166 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8195 (t0) REVERT: A 87 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7492 (ttp-170) REVERT: A 154 GLN cc_start: 0.7953 (tt0) cc_final: 0.7712 (tt0) REVERT: B 63 ASP cc_start: 0.7951 (t0) cc_final: 0.7691 (t0) REVERT: B 137 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6636 (tmm160) REVERT: B 202 GLU cc_start: 0.7416 (tt0) cc_final: 0.7133 (tt0) REVERT: B 246 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: B 358 GLN cc_start: 0.8407 (mt0) cc_final: 0.8184 (mm-40) REVERT: B 467 SER cc_start: 0.7108 (OUTLIER) cc_final: 0.6780 (m) REVERT: C 52 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6989 (tm) REVERT: C 247 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6749 (mtt-85) REVERT: C 251 ASP cc_start: 0.7836 (m-30) cc_final: 0.7164 (m-30) REVERT: D 49 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8217 (mt) REVERT: D 261 TRP cc_start: 0.8116 (m100) cc_final: 0.7829 (m100) REVERT: E 108 PHE cc_start: 0.7537 (m-80) cc_final: 0.6885 (m-10) REVERT: E 137 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6225 (tmm160) REVERT: E 246 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: E 375 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7513 (mtm180) REVERT: E 431 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8252 (m110) REVERT: E 467 SER cc_start: 0.7186 (OUTLIER) cc_final: 0.6822 (m) REVERT: E 503 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4872 (pt) REVERT: F 52 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7015 (tm) REVERT: F 247 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6832 (ttt-90) REVERT: F 251 ASP cc_start: 0.7840 (m-30) cc_final: 0.7175 (m-30) outliers start: 115 outliers final: 70 residues processed: 272 average time/residue: 0.3163 time to fit residues: 123.9036 Evaluate side-chains 228 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 146 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 53 optimal weight: 0.0060 chunk 194 optimal weight: 0.9980 chunk 210 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 211 GLN C 30 GLN C 51 HIS D 202 HIS D 211 GLN E 358 GLN F 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16764 Z= 0.168 Angle : 0.619 9.480 22808 Z= 0.312 Chirality : 0.042 0.157 2564 Planarity : 0.005 0.046 2962 Dihedral : 7.845 59.920 2433 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 6.11 % Allowed : 17.67 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.03 (0.18), residues: 2124 helix: 0.64 (0.20), residues: 766 sheet: -1.99 (0.26), residues: 398 loop : -2.79 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 360 HIS 0.003 0.001 HIS A 144 PHE 0.020 0.001 PHE A 68 TYR 0.010 0.001 TYR E 154 ARG 0.004 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 162 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8218 (mt) REVERT: A 154 GLN cc_start: 0.7846 (tt0) cc_final: 0.7585 (tt0) REVERT: A 206 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7220 (ttm170) REVERT: B 63 ASP cc_start: 0.7808 (t0) cc_final: 0.7536 (t0) REVERT: B 137 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6370 (tmm160) REVERT: B 202 GLU cc_start: 0.7380 (tt0) cc_final: 0.7050 (tt0) REVERT: B 246 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: B 267 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7542 (tttm) REVERT: B 286 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6346 (mm110) REVERT: B 405 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6365 (mm) REVERT: B 431 ASN cc_start: 0.8293 (m110) cc_final: 0.8012 (m-40) REVERT: B 467 SER cc_start: 0.6917 (OUTLIER) cc_final: 0.6574 (m) REVERT: B 503 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.4891 (pt) REVERT: C 247 ARG cc_start: 0.7165 (mtp85) cc_final: 0.6746 (mtp85) REVERT: C 251 ASP cc_start: 0.7732 (m-30) cc_final: 0.7049 (m-30) REVERT: D 49 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8207 (mt) REVERT: D 261 TRP cc_start: 0.8084 (m100) cc_final: 0.7794 (m100) REVERT: E 63 ASP cc_start: 0.7792 (t0) cc_final: 0.7470 (t0) REVERT: E 108 PHE cc_start: 0.7640 (m-80) cc_final: 0.6971 (m-10) REVERT: E 137 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.5987 (tmm160) REVERT: E 246 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: E 286 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6506 (mm110) REVERT: E 375 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7537 (mtm180) REVERT: E 467 SER cc_start: 0.7045 (OUTLIER) cc_final: 0.6567 (m) REVERT: E 503 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.4978 (pt) REVERT: F 247 ARG cc_start: 0.7097 (mtp85) cc_final: 0.6712 (ttt-90) REVERT: F 251 ASP cc_start: 0.7802 (m-30) cc_final: 0.7120 (m-30) outliers start: 103 outliers final: 66 residues processed: 256 average time/residue: 0.3110 time to fit residues: 115.0745 Evaluate side-chains 226 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 146 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 195 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 GLN C 30 GLN F 30 GLN F 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16764 Z= 0.372 Angle : 0.733 8.529 22808 Z= 0.365 Chirality : 0.046 0.175 2564 Planarity : 0.005 0.048 2962 Dihedral : 7.514 53.600 2417 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.99 % Favored : 86.86 % Rotamer: Outliers : 6.94 % Allowed : 17.50 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.13 (0.18), residues: 2124 helix: 0.63 (0.20), residues: 752 sheet: -2.20 (0.25), residues: 414 loop : -2.79 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 360 HIS 0.004 0.001 HIS E 215 PHE 0.016 0.002 PHE D 68 TYR 0.013 0.002 TYR A 32 ARG 0.006 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 149 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLN cc_start: 0.7962 (tt0) cc_final: 0.7759 (tt0) REVERT: B 63 ASP cc_start: 0.7914 (t0) cc_final: 0.7650 (t0) REVERT: B 137 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6456 (tmm160) REVERT: B 202 GLU cc_start: 0.7713 (tt0) cc_final: 0.7449 (tt0) REVERT: B 405 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6373 (mm) REVERT: B 486 ASN cc_start: 0.7727 (m-40) cc_final: 0.7449 (t0) REVERT: B 503 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.4901 (pt) REVERT: C 52 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7048 (tm) REVERT: D 30 ARG cc_start: 0.7061 (mtp85) cc_final: 0.6809 (mtp85) REVERT: D 49 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8105 (mt) REVERT: E 63 ASP cc_start: 0.7925 (t0) cc_final: 0.7652 (t0) REVERT: E 137 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6164 (tmm160) REVERT: E 205 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7591 (tpt170) REVERT: E 375 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7483 (mtm180) REVERT: E 486 ASN cc_start: 0.7539 (m-40) cc_final: 0.7306 (t0) REVERT: F 52 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7098 (tm) outliers start: 117 outliers final: 93 residues processed: 256 average time/residue: 0.3079 time to fit residues: 115.9367 Evaluate side-chains 243 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 142 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN E 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16764 Z= 0.255 Angle : 0.660 7.292 22808 Z= 0.331 Chirality : 0.044 0.158 2564 Planarity : 0.005 0.047 2962 Dihedral : 7.197 54.818 2408 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.35 % Favored : 88.42 % Rotamer: Outliers : 6.29 % Allowed : 18.68 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.88 (0.18), residues: 2124 helix: 0.90 (0.20), residues: 750 sheet: -1.91 (0.26), residues: 398 loop : -2.78 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 360 HIS 0.007 0.001 HIS F 172 PHE 0.012 0.001 PHE B 100 TYR 0.013 0.001 TYR E 154 ARG 0.006 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 156 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLN cc_start: 0.7909 (tt0) cc_final: 0.7696 (tt0) REVERT: B 137 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.6297 (tmm160) REVERT: B 202 GLU cc_start: 0.7640 (tt0) cc_final: 0.7383 (tt0) REVERT: B 286 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6488 (mm110) REVERT: B 405 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6313 (mm) REVERT: B 486 ASN cc_start: 0.7647 (m-40) cc_final: 0.7445 (t0) REVERT: B 503 LEU cc_start: 0.5231 (OUTLIER) cc_final: 0.4845 (pt) REVERT: C 52 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7118 (tm) REVERT: D 30 ARG cc_start: 0.7112 (mtp85) cc_final: 0.6844 (mtp85) REVERT: D 49 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8088 (mt) REVERT: E 63 ASP cc_start: 0.7817 (t0) cc_final: 0.7600 (t0) REVERT: E 137 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6034 (tmm160) REVERT: E 286 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6567 (mm110) REVERT: E 375 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7499 (mtm180) REVERT: E 431 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8091 (m110) REVERT: F 52 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7166 (tm) outliers start: 106 outliers final: 86 residues processed: 254 average time/residue: 0.3090 time to fit residues: 113.5277 Evaluate side-chains 245 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 149 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 207 optimal weight: 0.3980 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16764 Z= 0.164 Angle : 0.612 7.382 22808 Z= 0.308 Chirality : 0.042 0.156 2564 Planarity : 0.005 0.047 2962 Dihedral : 6.916 55.660 2404 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.11 % Favored : 88.79 % Rotamer: Outliers : 6.29 % Allowed : 18.74 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.49 (0.19), residues: 2124 helix: 1.28 (0.20), residues: 750 sheet: -1.61 (0.27), residues: 386 loop : -2.64 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 360 HIS 0.006 0.001 HIS F 172 PHE 0.010 0.001 PHE A 103 TYR 0.008 0.001 TYR A 32 ARG 0.007 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 163 time to evaluate : 1.831 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8061 (mt) REVERT: A 154 GLN cc_start: 0.7794 (tt0) cc_final: 0.7574 (tt0) REVERT: A 206 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7252 (ttm170) REVERT: B 137 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.6409 (tmm160) REVERT: B 202 GLU cc_start: 0.7625 (tt0) cc_final: 0.7376 (tt0) REVERT: B 246 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: B 286 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6434 (mm110) REVERT: B 405 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6332 (mm) REVERT: B 503 LEU cc_start: 0.5290 (OUTLIER) cc_final: 0.4867 (pt) REVERT: C 52 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7044 (tm) REVERT: C 247 ARG cc_start: 0.7210 (mtt-85) cc_final: 0.6331 (mtp85) REVERT: C 251 ASP cc_start: 0.7814 (m-30) cc_final: 0.7053 (m-30) REVERT: D 30 ARG cc_start: 0.7099 (mtp85) cc_final: 0.6805 (mtp85) REVERT: D 49 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8134 (mt) REVERT: E 137 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6196 (tmm160) REVERT: E 246 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: E 286 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6586 (mm110) REVERT: E 375 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7490 (mtm180) REVERT: F 52 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7007 (tm) REVERT: F 247 ARG cc_start: 0.7190 (mtt-85) cc_final: 0.6593 (mtt-85) REVERT: F 251 ASP cc_start: 0.7820 (m-30) cc_final: 0.7094 (m-30) outliers start: 106 outliers final: 84 residues processed: 262 average time/residue: 0.3133 time to fit residues: 118.8295 Evaluate side-chains 252 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 156 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 115 optimal weight: 0.4980 chunk 206 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16764 Z= 0.210 Angle : 0.626 6.710 22808 Z= 0.315 Chirality : 0.042 0.150 2564 Planarity : 0.005 0.047 2962 Dihedral : 6.894 55.705 2404 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.30 % Favored : 88.61 % Rotamer: Outliers : 6.64 % Allowed : 18.68 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.41 (0.19), residues: 2124 helix: 1.35 (0.20), residues: 750 sheet: -1.53 (0.27), residues: 386 loop : -2.61 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 360 HIS 0.006 0.001 HIS F 172 PHE 0.010 0.001 PHE B 100 TYR 0.013 0.001 TYR E 154 ARG 0.007 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 161 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8018 (mt) REVERT: A 154 GLN cc_start: 0.7818 (tt0) cc_final: 0.7610 (tt0) REVERT: A 206 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7242 (ttm170) REVERT: B 137 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6428 (tmm160) REVERT: B 202 GLU cc_start: 0.7648 (tt0) cc_final: 0.7397 (tt0) REVERT: B 246 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: B 286 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6465 (mm110) REVERT: B 405 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6272 (mm) REVERT: B 503 LEU cc_start: 0.5232 (OUTLIER) cc_final: 0.4804 (pt) REVERT: C 52 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7047 (tm) REVERT: C 247 ARG cc_start: 0.7283 (mtt-85) cc_final: 0.6944 (mtp85) REVERT: D 49 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8055 (mt) REVERT: E 137 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6338 (tmm160) REVERT: E 246 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: E 286 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6575 (mm110) REVERT: E 375 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7459 (mtm180) REVERT: F 52 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7039 (tm) outliers start: 112 outliers final: 89 residues processed: 266 average time/residue: 0.3080 time to fit residues: 119.9665 Evaluate side-chains 257 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 156 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16764 Z= 0.366 Angle : 0.728 9.678 22808 Z= 0.362 Chirality : 0.046 0.179 2564 Planarity : 0.005 0.048 2962 Dihedral : 7.282 54.332 2404 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.04 % Favored : 86.82 % Rotamer: Outliers : 7.24 % Allowed : 18.09 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.72 (0.18), residues: 2124 helix: 1.09 (0.20), residues: 738 sheet: -1.76 (0.26), residues: 384 loop : -2.71 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 360 HIS 0.007 0.001 HIS F 172 PHE 0.015 0.002 PHE D 68 TYR 0.014 0.002 TYR A 32 ARG 0.006 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 155 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8008 (mt) REVERT: B 137 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6407 (tmm160) REVERT: B 202 GLU cc_start: 0.7768 (tt0) cc_final: 0.7534 (tt0) REVERT: B 405 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6193 (mm) REVERT: B 503 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.4834 (pt) REVERT: C 52 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7193 (tm) REVERT: C 247 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.7046 (mtp85) REVERT: D 30 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6859 (mtp85) REVERT: D 49 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8084 (mt) REVERT: E 137 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6148 (tmm160) REVERT: E 375 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7361 (mtm180) REVERT: F 52 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7197 (tm) outliers start: 122 outliers final: 102 residues processed: 267 average time/residue: 0.2988 time to fit residues: 117.2243 Evaluate side-chains 261 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 151 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 chunk 115 optimal weight: 0.0770 chunk 83 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 191 optimal weight: 0.5980 chunk 126 optimal weight: 0.2980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 486 ASN C 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16764 Z= 0.160 Angle : 0.615 13.339 22808 Z= 0.309 Chirality : 0.042 0.159 2564 Planarity : 0.005 0.046 2962 Dihedral : 6.870 56.528 2404 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 5.63 % Allowed : 19.93 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.27 (0.19), residues: 2124 helix: 1.45 (0.20), residues: 752 sheet: -1.42 (0.27), residues: 386 loop : -2.54 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 360 HIS 0.007 0.001 HIS C 172 PHE 0.011 0.001 PHE A 103 TYR 0.010 0.001 TYR E 154 ARG 0.006 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 159 time to evaluate : 1.832 Fit side-chains REVERT: A 49 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7956 (mt) REVERT: A 206 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7187 (ttm170) REVERT: B 105 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 137 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6406 (tmm160) REVERT: B 202 GLU cc_start: 0.7613 (tt0) cc_final: 0.7365 (tt0) REVERT: B 246 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: B 286 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6505 (mm110) REVERT: B 405 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6091 (mm) REVERT: B 503 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4821 (pt) REVERT: C 52 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6947 (tm) REVERT: C 247 ARG cc_start: 0.7282 (mtt-85) cc_final: 0.6474 (mtp85) REVERT: C 251 ASP cc_start: 0.7789 (m-30) cc_final: 0.7145 (m-30) REVERT: C 300 TYR cc_start: 0.8499 (m-80) cc_final: 0.8277 (m-80) REVERT: D 49 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8118 (mt) REVERT: E 137 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6401 (tmm160) REVERT: E 246 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: E 286 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6641 (mm110) REVERT: E 375 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7554 (mtm180) REVERT: F 52 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6927 (tm) REVERT: F 247 ARG cc_start: 0.7293 (mtt-85) cc_final: 0.6444 (mtp85) REVERT: F 251 ASP cc_start: 0.7828 (m-30) cc_final: 0.7081 (m-30) outliers start: 95 outliers final: 75 residues processed: 246 average time/residue: 0.3140 time to fit residues: 111.8202 Evaluate side-chains 240 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 152 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.0040 chunk 124 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 213 optimal weight: 0.0170 chunk 196 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.5032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16764 Z= 0.148 Angle : 0.606 13.835 22808 Z= 0.302 Chirality : 0.042 0.176 2564 Planarity : 0.004 0.046 2962 Dihedral : 6.637 56.482 2403 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 5.34 % Allowed : 20.05 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.11 (0.19), residues: 2124 helix: 1.66 (0.20), residues: 750 sheet: -1.25 (0.28), residues: 376 loop : -2.53 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.005 0.001 HIS F 172 PHE 0.011 0.001 PHE A 103 TYR 0.008 0.001 TYR C 300 ARG 0.005 0.000 ARG A 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 165 time to evaluate : 1.896 Fit side-chains REVERT: A 49 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7878 (mt) REVERT: A 206 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7187 (ttm170) REVERT: B 137 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6663 (tmm160) REVERT: B 180 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6998 (mtm110) REVERT: B 202 GLU cc_start: 0.7630 (tt0) cc_final: 0.7377 (tt0) REVERT: B 246 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: B 286 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6553 (mm110) REVERT: B 503 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4898 (pt) REVERT: C 52 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6950 (tm) REVERT: C 247 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6460 (mtp85) REVERT: C 251 ASP cc_start: 0.7716 (m-30) cc_final: 0.7003 (m-30) REVERT: D 49 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8051 (mt) REVERT: E 105 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7624 (t80) REVERT: E 137 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6670 (tmm160) REVERT: E 246 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: E 286 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6619 (mm110) REVERT: E 375 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7353 (mtm180) REVERT: F 52 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6893 (tm) REVERT: F 247 ARG cc_start: 0.7325 (mtt-85) cc_final: 0.6467 (mtp85) REVERT: F 251 ASP cc_start: 0.7757 (m-30) cc_final: 0.7060 (m-30) REVERT: F 368 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7506 (ttm-80) outliers start: 90 outliers final: 72 residues processed: 251 average time/residue: 0.3144 time to fit residues: 114.4851 Evaluate side-chains 233 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 149 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 105 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 47 optimal weight: 1.9990 chunk 170 optimal weight: 0.0050 chunk 71 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.168543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.131644 restraints weight = 18546.401| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.17 r_work: 0.3272 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16764 Z= 0.238 Angle : 0.649 13.782 22808 Z= 0.322 Chirality : 0.043 0.180 2564 Planarity : 0.005 0.047 2962 Dihedral : 6.664 55.741 2399 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 5.46 % Allowed : 19.99 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.18 (0.19), residues: 2124 helix: 1.57 (0.20), residues: 752 sheet: -1.29 (0.27), residues: 386 loop : -2.56 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 360 HIS 0.005 0.001 HIS F 172 PHE 0.011 0.001 PHE E 100 TYR 0.014 0.001 TYR B 154 ARG 0.004 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3743.52 seconds wall clock time: 68 minutes 17.24 seconds (4097.24 seconds total)