Starting phenix.real_space_refine on Mon Dec 11 02:29:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/12_2023/6wul_21915.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/12_2023/6wul_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_21915/12_2023/6wul_21915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/12_2023/6wul_21915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/12_2023/6wul_21915.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wul_21915/12_2023/6wul_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-1.21rc1-5172/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: 8.96, per 1000 atoms: 0.55 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: 6.42 Conformation dependent library (CDL) restraints added in 3.1 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: 1.77 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: 4.95 Time building geometry restraints manager: 6.86 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: 1.030 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: 3.370 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 44.790 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.260 ------------------------------------------------------------------------------- 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 : 1.966 Fit side-chains revert: symmetry clash outliers start: 118 outliers final: 75 residues processed: 323 average time/residue: 0.3637 time to fit residues: 164.0254 Evaluate side-chains 242 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 167 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.1513 time to fit residues: 23.7583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 55 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 A 310 ASN B 148 ASN B 286 GLN B 358 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 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: 0.7716 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16764 Z= 0.322 Angle : 0.740 8.667 22808 Z= 0.371 Chirality : 0.046 0.239 2564 Planarity : 0.005 0.048 2962 Dihedral : 5.867 30.825 2356 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.62 % Favored : 87.24 % Rotamer: Outliers : 3.97 % Allowed : 17.50 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.80 (0.17), residues: 2124 helix: -0.13 (0.19), residues: 762 sheet: -2.50 (0.24), residues: 392 loop : -3.05 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 360 HIS 0.005 0.001 HIS B 215 PHE 0.019 0.002 PHE D 262 TYR 0.014 0.002 TYR A 32 ARG 0.005 0.000 ARG F 368 *********************** 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 224 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 157 time to evaluate : 1.822 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 40 residues processed: 216 average time/residue: 0.3584 time to fit residues: 109.9874 Evaluate side-chains 184 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.1505 time to fit residues: 13.8731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 193 optimal weight: 0.3980 chunk 66 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS A 211 GLN C 30 GLN D 202 HIS D 211 GLN E 286 GLN F 30 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1620 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 : 0.646 6.843 22808 Z= 0.326 Chirality : 0.043 0.188 2564 Planarity : 0.005 0.047 2962 Dihedral : 5.510 31.066 2356 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.78 % Favored : 89.08 % Rotamer: Outliers : 3.14 % Allowed : 18.03 % Favored : 78.83 % 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: -2.18 (0.18), residues: 2124 helix: 0.51 (0.20), residues: 760 sheet: -2.03 (0.26), residues: 390 loop : -2.87 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 360 HIS 0.003 0.001 HIS C 51 PHE 0.013 0.001 PHE D 262 TYR 0.010 0.001 TYR E 154 ARG 0.010 0.000 ARG B 426 *********************** 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 212 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 159 time to evaluate : 1.799 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 31 residues processed: 208 average time/residue: 0.3284 time to fit residues: 98.5035 Evaluate side-chains 174 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1457 time to fit residues: 10.7999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN C 30 GLN C 51 HIS D 211 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16764 Z= 0.422 Angle : 0.778 11.169 22808 Z= 0.387 Chirality : 0.048 0.258 2564 Planarity : 0.006 0.051 2962 Dihedral : 5.872 32.116 2356 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.79 % Favored : 86.06 % Rotamer: Outliers : 2.55 % Allowed : 19.63 % Favored : 77.82 % 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: -2.35 (0.18), residues: 2124 helix: 0.37 (0.19), residues: 760 sheet: -2.33 (0.25), residues: 408 loop : -2.86 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 8 HIS 0.005 0.001 HIS E 215 PHE 0.014 0.002 PHE E 100 TYR 0.015 0.002 TYR A 32 ARG 0.007 0.000 ARG D 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 190 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 1.759 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 33 residues processed: 184 average time/residue: 0.3436 time to fit residues: 92.9818 Evaluate side-chains 170 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.634 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1486 time to fit residues: 11.5325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16764 Z= 0.186 Angle : 0.638 7.732 22808 Z= 0.321 Chirality : 0.043 0.175 2564 Planarity : 0.005 0.048 2962 Dihedral : 5.418 30.849 2356 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.69 % Favored : 89.22 % Rotamer: Outliers : 0.89 % Allowed : 20.17 % Favored : 78.94 % 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: -1.79 (0.18), residues: 2124 helix: 0.99 (0.20), residues: 746 sheet: -1.81 (0.26), residues: 394 loop : -2.75 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 291 HIS 0.009 0.001 HIS C 172 PHE 0.014 0.001 PHE B 100 TYR 0.010 0.001 TYR E 154 ARG 0.004 0.000 ARG D 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 174 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.902 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 171 average time/residue: 0.3929 time to fit residues: 96.1065 Evaluate side-chains 151 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1509 time to fit residues: 4.0953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 9.9990 chunk 186 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 0.0040 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 GLN ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16764 Z= 0.304 Angle : 0.692 8.729 22808 Z= 0.345 Chirality : 0.045 0.204 2564 Planarity : 0.005 0.049 2962 Dihedral : 5.554 31.987 2356 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.76 % Favored : 87.10 % Rotamer: Outliers : 2.02 % Allowed : 20.34 % Favored : 77.64 % 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: -1.83 (0.18), residues: 2124 helix: 0.96 (0.20), residues: 746 sheet: -1.86 (0.26), residues: 386 loop : -2.76 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 360 HIS 0.010 0.001 HIS F 172 PHE 0.013 0.002 PHE E 100 TYR 0.014 0.001 TYR B 154 ARG 0.008 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 183 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 1.707 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 175 average time/residue: 0.3393 time to fit residues: 86.2506 Evaluate side-chains 161 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 2.000 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1609 time to fit residues: 8.1088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 115 optimal weight: 0.0370 chunk 206 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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** ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16764 Z= 0.168 Angle : 0.618 7.981 22808 Z= 0.311 Chirality : 0.042 0.158 2564 Planarity : 0.005 0.047 2962 Dihedral : 5.230 30.775 2356 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 1.13 % Allowed : 20.52 % Favored : 78.35 % 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: -1.44 (0.19), residues: 2124 helix: 1.28 (0.20), residues: 756 sheet: -1.50 (0.27), residues: 382 loop : -2.63 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 360 HIS 0.010 0.001 HIS C 172 PHE 0.010 0.001 PHE A 103 TYR 0.011 0.001 TYR F 300 ARG 0.006 0.000 ARG C 247 *********************** 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 183 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.922 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 180 average time/residue: 0.3442 time to fit residues: 90.3910 Evaluate side-chains 160 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1564 time to fit residues: 4.9577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7735 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16764 Z= 0.395 Angle : 0.744 8.982 22808 Z= 0.371 Chirality : 0.047 0.218 2564 Planarity : 0.005 0.049 2962 Dihedral : 5.686 33.328 2356 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.90 % Favored : 86.96 % Rotamer: Outliers : 1.42 % Allowed : 20.64 % Favored : 77.94 % 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: -1.84 (0.18), residues: 2124 helix: 0.90 (0.19), residues: 744 sheet: -1.80 (0.26), residues: 384 loop : -2.73 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 8 HIS 0.009 0.001 HIS F 172 PHE 0.014 0.002 PHE E 100 TYR 0.017 0.002 TYR B 154 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 168 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.847 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 166 average time/residue: 0.3260 time to fit residues: 79.5970 Evaluate side-chains 153 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1467 time to fit residues: 6.2257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 192 optimal weight: 0.8980 chunk 115 optimal weight: 0.0370 chunk 83 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16764 Z= 0.165 Angle : 0.622 7.378 22808 Z= 0.315 Chirality : 0.042 0.167 2564 Planarity : 0.005 0.047 2962 Dihedral : 5.236 31.087 2356 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.30 % Allowed : 21.23 % Favored : 78.47 % 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: -1.41 (0.19), residues: 2124 helix: 1.29 (0.20), residues: 756 sheet: -1.47 (0.27), residues: 382 loop : -2.60 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 291 HIS 0.010 0.001 HIS F 172 PHE 0.011 0.001 PHE A 103 TYR 0.013 0.001 TYR C 300 ARG 0.004 0.000 ARG A 30 *********************** 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 158 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.880 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 156 average time/residue: 0.3635 time to fit residues: 81.6115 Evaluate side-chains 147 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1433 time to fit residues: 3.0877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 213 optimal weight: 0.0050 chunk 196 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16764 Z= 0.198 Angle : 0.631 6.543 22808 Z= 0.316 Chirality : 0.043 0.192 2564 Planarity : 0.005 0.047 2962 Dihedral : 5.186 30.919 2356 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 0.24 % Allowed : 21.29 % Favored : 78.47 % 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: -1.39 (0.19), residues: 2124 helix: 1.43 (0.20), residues: 744 sheet: -1.47 (0.27), residues: 386 loop : -2.65 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 360 HIS 0.009 0.001 HIS C 172 PHE 0.010 0.001 PHE A 103 TYR 0.010 0.001 TYR F 37 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 151 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 1.894 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 150 average time/residue: 0.3665 time to fit residues: 78.2592 Evaluate side-chains 145 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.719 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1733 time to fit residues: 2.9717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.0020 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 174 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 149 optimal weight: 4.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.172464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134927 restraints weight = 18519.239| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.26 r_work: 0.3305 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2566 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= 0.158 Angle : 0.600 6.178 22808 Z= 0.303 Chirality : 0.042 0.167 2564 Planarity : 0.005 0.046 2962 Dihedral : 4.999 31.302 2356 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.24 % Allowed : 21.41 % Favored : 78.35 % 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: -1.17 (0.19), residues: 2124 helix: 1.55 (0.20), residues: 756 sheet: -1.25 (0.27), residues: 392 loop : -2.57 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 291 HIS 0.010 0.001 HIS F 172 PHE 0.010 0.001 PHE A 103 TYR 0.012 0.001 TYR E 154 ARG 0.005 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.83 seconds wall clock time: 60 minutes 47.53 seconds (3647.53 seconds total)