Starting phenix.real_space_refine on Mon Mar 18 10:21:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl0_27494/03_2024/8dl0_27494.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl0_27494/03_2024/8dl0_27494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl0_27494/03_2024/8dl0_27494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl0_27494/03_2024/8dl0_27494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl0_27494/03_2024/8dl0_27494.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dl0_27494/03_2024/8dl0_27494.pdb" } resolution = 4.1 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= 0.002 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10294 atoms to isotropic. 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 32 5.16 5 C 6922 2.51 5 N 1627 2.21 5 O 1796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 3": "NH1" <-> "NH2" Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 19": "OD1" <-> "OD2" Residue "A PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 354": "OD1" <-> "OD2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 251": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10377 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3078 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2126 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain: "C" Number of atoms: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3047 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 12, 'TRANS': 365} Chain breaks: 1 Chain: "D" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2126 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Time building chain proxies: 5.66, per 1000 atoms: 0.55 Number of scatterers: 10377 At special positions: 0 Unit cell: (96.12, 87.48, 140.4, 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 32 16.00 O 1796 8.00 N 1627 7.00 C 6922 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: 4.06 Conformation dependent library (CDL) restraints added in 1.8 seconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 53.9% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 removed outlier: 3.780A pdb=" N LEU A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.536A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.621A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.744A pdb=" N ASN A 136 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.675A pdb=" N ALA A 170 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 190 removed outlier: 3.633A pdb=" N LYS A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 43 removed outlier: 3.580A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 88 Proline residue: B 70 - end of helix removed outlier: 3.722A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N THR B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 100 through 129 removed outlier: 3.552A pdb=" N VAL B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.998A pdb=" N TYR B 136 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR B 138 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 165 removed outlier: 4.333A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 144 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.519A pdb=" N ILE B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.618A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.585A pdb=" N VAL B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.589A pdb=" N LEU B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 5.052A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 removed outlier: 4.294A pdb=" N ILE C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.938A pdb=" N THR C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 114 through 130 removed outlier: 4.764A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.860A pdb=" N ASN C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.509A pdb=" N ILE C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 189 Processing helix chain 'C' and resid 200 through 208 Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 29 through 43 Processing helix chain 'D' and resid 54 through 84 Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.976A pdb=" N LYS D 89 " --> pdb=" O PHE D 85 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 129 removed outlier: 3.822A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 removed outlier: 3.611A pdb=" N LYS D 135 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 136 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 164 removed outlier: 4.280A pdb=" N LEU D 144 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 183 removed outlier: 3.677A pdb=" N ILE D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 removed outlier: 3.876A pdb=" N ILE D 191 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 202 removed outlier: 3.843A pdb=" N TYR D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 218 removed outlier: 4.238A pdb=" N VAL D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 255 Proline residue: D 235 - end of helix removed outlier: 4.843A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 43 removed outlier: 5.677A pdb=" N GLU A 33 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR A 13 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TRP A 35 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR A 11 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 7 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN A 41 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE A 5 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 43 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG A 3 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.198A pdb=" N VAL A 85 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 211 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU A 222 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 213 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 220 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 265 removed outlier: 6.486A pdb=" N ASP A 285 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 262 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU A 283 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 264 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 281 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 326 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS A 327 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 394 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 276 removed outlier: 6.352A pdb=" N PHE A 274 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY A 373 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N CYS A 359 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 351 " --> pdb=" O CYS A 359 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 347 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 365 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 345 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N CYS A 367 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR A 343 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE A 369 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY A 341 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 310 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP A 303 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 394 removed outlier: 4.276A pdb=" N LYS C 327 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 43 removed outlier: 5.409A pdb=" N GLU C 33 " --> pdb=" O TYR C 13 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR C 13 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TRP C 35 " --> pdb=" O TYR C 11 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR C 11 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL C 7 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C 41 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE C 5 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU C 43 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ARG C 3 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 5 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 77 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL C 7 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS C 75 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.261A pdb=" N VAL C 85 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE C 163 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL C 197 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 165 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU C 50 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA C 211 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU C 222 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU C 213 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 276 removed outlier: 6.340A pdb=" N PHE C 274 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY C 373 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N CYS C 359 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS C 351 " --> pdb=" O CYS C 359 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 347 " --> pdb=" O ILE C 363 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 365 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU C 345 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N CYS C 367 " --> pdb=" O TYR C 343 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR C 343 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE C 369 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY C 341 " --> pdb=" O PHE C 369 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 4.37 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: 3107 1.34 - 1.46: 2420 1.46 - 1.58: 5070 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 10649 Sorted by residual: bond pdb=" N GLU C 358 " pdb=" CA GLU C 358 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.46e+00 bond pdb=" N TYR A 391 " pdb=" CA TYR A 391 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.49e+00 bond pdb=" N ASN A 390 " pdb=" CA ASN A 390 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.20e-02 6.94e+03 6.13e+00 bond pdb=" N MET C 317 " pdb=" CA MET C 317 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.33e-02 5.65e+03 4.73e+00 bond pdb=" N CYS C 359 " pdb=" CA CYS C 359 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.46e-02 4.69e+03 4.34e+00 ... (remaining 10644 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.27: 161 105.27 - 112.46: 5388 112.46 - 119.64: 3452 119.64 - 126.82: 5277 126.82 - 134.01: 124 Bond angle restraints: 14402 Sorted by residual: angle pdb=" N LEU C 316 " pdb=" CA LEU C 316 " pdb=" C LEU C 316 " ideal model delta sigma weight residual 113.01 106.53 6.48 1.20e+00 6.94e-01 2.92e+01 angle pdb=" N ILE A 394 " pdb=" CA ILE A 394 " pdb=" C ILE A 394 " ideal model delta sigma weight residual 107.61 113.83 -6.22 1.19e+00 7.06e-01 2.73e+01 angle pdb=" N ILE A 394 " pdb=" CA ILE A 394 " pdb=" CB ILE A 394 " ideal model delta sigma weight residual 112.37 106.87 5.50 1.06e+00 8.90e-01 2.69e+01 angle pdb=" N GLU D 13 " pdb=" CA GLU D 13 " pdb=" CB GLU D 13 " ideal model delta sigma weight residual 110.16 116.62 -6.46 1.48e+00 4.57e-01 1.91e+01 angle pdb=" C GLU C 358 " pdb=" CA GLU C 358 " pdb=" CB GLU C 358 " ideal model delta sigma weight residual 110.42 102.24 8.18 1.99e+00 2.53e-01 1.69e+01 ... (remaining 14397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5694 17.73 - 35.47: 461 35.47 - 53.20: 65 53.20 - 70.93: 11 70.93 - 88.66: 9 Dihedral angle restraints: 6240 sinusoidal: 2544 harmonic: 3696 Sorted by residual: dihedral pdb=" C GLU C 358 " pdb=" N GLU C 358 " pdb=" CA GLU C 358 " pdb=" CB GLU C 358 " ideal model delta harmonic sigma weight residual -122.60 -112.57 -10.03 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" C LYS A 393 " pdb=" N LYS A 393 " pdb=" CA LYS A 393 " pdb=" CB LYS A 393 " ideal model delta harmonic sigma weight residual -122.60 -113.45 -9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N GLY B 52 " pdb=" CA GLY B 52 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 6237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1387 0.064 - 0.127: 209 0.127 - 0.191: 15 0.191 - 0.254: 3 0.254 - 0.318: 1 Chirality restraints: 1615 Sorted by residual: chirality pdb=" CA GLU C 358 " pdb=" N GLU C 358 " pdb=" C GLU C 358 " pdb=" CB GLU C 358 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA MET C 317 " pdb=" N MET C 317 " pdb=" C MET C 317 " pdb=" CB MET C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA LYS A 393 " pdb=" N LYS A 393 " pdb=" C LYS A 393 " pdb=" CB LYS A 393 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1612 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 9 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C LEU D 9 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU D 9 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL D 10 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 244 " 0.013 2.00e-02 2.50e+03 1.40e-02 3.44e+00 pdb=" CG PHE B 244 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 244 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 244 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 244 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 244 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 244 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 358 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C GLU C 358 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU C 358 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS C 359 " 0.011 2.00e-02 2.50e+03 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 376 2.71 - 3.26: 10942 3.26 - 3.81: 17269 3.81 - 4.35: 20621 4.35 - 4.90: 34237 Nonbonded interactions: 83445 Sorted by model distance: nonbonded pdb=" NH1 ARG A 392 " pdb=" O LYS A 393 " model vdw 2.168 2.520 nonbonded pdb=" OG1 THR D 188 " pdb=" OH TYR D 219 " model vdw 2.221 2.440 nonbonded pdb=" O LEU D 192 " pdb=" NZ LYS D 197 " model vdw 2.222 2.520 nonbonded pdb=" O GLY D 83 " pdb=" OG1 THR D 86 " model vdw 2.236 2.440 nonbonded pdb=" O PRO A 138 " pdb=" OG1 THR A 141 " model vdw 2.240 2.440 ... (remaining 83440 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' and (resid 2 through 237 or resid 254 through 395)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 4.080 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.990 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 0.003 0.040 10649 Z= 0.177 Angle : 0.668 8.185 14402 Z= 0.385 Chirality : 0.045 0.318 1615 Planarity : 0.003 0.032 1768 Dihedral : 13.217 88.664 3872 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1256 helix: 1.31 (0.22), residues: 579 sheet: 1.13 (0.39), residues: 176 loop : -1.62 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 26 HIS 0.007 0.001 HIS A 361 PHE 0.032 0.001 PHE B 244 TYR 0.014 0.001 TYR D 18 ARG 0.005 0.001 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8033 (m90) cc_final: 0.7515 (m90) REVERT: A 178 GLN cc_start: 0.8430 (tp-100) cc_final: 0.8014 (tp40) REVERT: B 53 HIS cc_start: 0.8245 (m-70) cc_final: 0.7972 (m-70) REVERT: B 76 ASN cc_start: 0.8180 (t0) cc_final: 0.7807 (t0) REVERT: B 89 LYS cc_start: 0.9479 (ptmt) cc_final: 0.9090 (tttt) REVERT: B 93 THR cc_start: 0.9132 (p) cc_final: 0.8922 (p) REVERT: B 110 GLU cc_start: 0.8402 (tp30) cc_final: 0.8165 (tp30) REVERT: B 113 ASN cc_start: 0.8539 (p0) cc_final: 0.8279 (p0) REVERT: B 169 LYS cc_start: 0.8925 (ptmm) cc_final: 0.8671 (tptp) REVERT: B 206 TYR cc_start: 0.8138 (t80) cc_final: 0.7863 (t80) REVERT: B 219 TYR cc_start: 0.7320 (t80) cc_final: 0.6719 (t80) REVERT: B 236 LEU cc_start: 0.9107 (tp) cc_final: 0.8870 (tp) REVERT: C 98 LEU cc_start: 0.8571 (mm) cc_final: 0.8320 (mm) REVERT: C 334 MET cc_start: 0.6261 (tpt) cc_final: 0.6030 (tpt) REVERT: D 80 ARG cc_start: 0.8707 (tmm-80) cc_final: 0.8323 (ttp-170) REVERT: D 88 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8705 (mmmt) REVERT: D 91 LEU cc_start: 0.9214 (mt) cc_final: 0.8894 (mt) REVERT: D 205 MET cc_start: 0.8759 (mmm) cc_final: 0.8445 (mmm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1860 time to fit residues: 51.1732 Evaluate side-chains 137 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN B 213 HIS C 175 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10649 Z= 0.267 Angle : 0.620 7.371 14402 Z= 0.329 Chirality : 0.043 0.141 1615 Planarity : 0.004 0.048 1768 Dihedral : 4.840 18.854 1364 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.18 % Allowed : 4.22 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1256 helix: 1.00 (0.21), residues: 592 sheet: 0.95 (0.39), residues: 187 loop : -1.45 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 362 HIS 0.009 0.002 HIS D 213 PHE 0.023 0.002 PHE D 72 TYR 0.018 0.002 TYR D 138 ARG 0.009 0.001 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8024 (m90) cc_final: 0.7502 (m90) REVERT: A 178 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8162 (tp40) REVERT: B 76 ASN cc_start: 0.8333 (t0) cc_final: 0.8030 (t0) REVERT: B 169 LYS cc_start: 0.9004 (ptmm) cc_final: 0.8753 (tptp) REVERT: B 206 TYR cc_start: 0.8238 (t80) cc_final: 0.8036 (t80) REVERT: B 219 TYR cc_start: 0.7307 (t80) cc_final: 0.6775 (t80) REVERT: C 95 ASN cc_start: 0.8943 (t0) cc_final: 0.8703 (t0) REVERT: C 98 LEU cc_start: 0.8471 (mm) cc_final: 0.8018 (mm) REVERT: C 178 GLN cc_start: 0.8853 (pt0) cc_final: 0.8460 (pp30) REVERT: C 334 MET cc_start: 0.6695 (tpt) cc_final: 0.6470 (tpt) REVERT: D 80 ARG cc_start: 0.8672 (tmm-80) cc_final: 0.8133 (ttp-170) REVERT: D 88 LYS cc_start: 0.9339 (mmmt) cc_final: 0.9133 (mmmt) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.2129 time to fit residues: 51.0898 Evaluate side-chains 125 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10649 Z= 0.213 Angle : 0.566 7.641 14402 Z= 0.299 Chirality : 0.042 0.137 1615 Planarity : 0.004 0.059 1768 Dihedral : 4.770 18.678 1364 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1256 helix: 1.01 (0.22), residues: 592 sheet: 0.94 (0.39), residues: 187 loop : -1.43 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 26 HIS 0.010 0.001 HIS B 213 PHE 0.024 0.002 PHE A 152 TYR 0.018 0.001 TYR D 138 ARG 0.010 0.001 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8066 (m90) cc_final: 0.7518 (m90) REVERT: A 178 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8175 (tp40) REVERT: B 76 ASN cc_start: 0.8345 (t0) cc_final: 0.7843 (t0) REVERT: B 110 GLU cc_start: 0.8492 (tp30) cc_final: 0.8117 (tp30) REVERT: B 113 ASN cc_start: 0.8539 (p0) cc_final: 0.8252 (p0) REVERT: B 114 TYR cc_start: 0.8318 (t80) cc_final: 0.7460 (t80) REVERT: B 169 LYS cc_start: 0.8972 (ptmm) cc_final: 0.8725 (tptp) REVERT: B 206 TYR cc_start: 0.8224 (t80) cc_final: 0.8024 (t80) REVERT: B 219 TYR cc_start: 0.7338 (t80) cc_final: 0.6733 (t80) REVERT: C 95 ASN cc_start: 0.8952 (t0) cc_final: 0.8654 (t0) REVERT: C 98 LEU cc_start: 0.8437 (mm) cc_final: 0.7965 (mm) REVERT: C 178 GLN cc_start: 0.8781 (pt0) cc_final: 0.8398 (pp30) REVERT: C 334 MET cc_start: 0.6741 (tpt) cc_final: 0.6514 (tpt) REVERT: D 13 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8686 (tm-30) REVERT: D 88 LYS cc_start: 0.9372 (mmmt) cc_final: 0.9167 (mmmt) REVERT: D 91 LEU cc_start: 0.9310 (mt) cc_final: 0.9100 (mt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1948 time to fit residues: 48.5729 Evaluate side-chains 123 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.0030 chunk 76 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10649 Z= 0.194 Angle : 0.561 8.067 14402 Z= 0.294 Chirality : 0.042 0.141 1615 Planarity : 0.004 0.038 1768 Dihedral : 4.722 18.644 1364 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1256 helix: 0.99 (0.21), residues: 594 sheet: 1.11 (0.40), residues: 174 loop : -1.48 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 26 HIS 0.008 0.001 HIS B 213 PHE 0.024 0.002 PHE A 152 TYR 0.017 0.001 TYR D 138 ARG 0.007 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8923 (ptpp) cc_final: 0.8693 (pttm) REVERT: A 157 HIS cc_start: 0.8114 (m90) cc_final: 0.7559 (m90) REVERT: A 178 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8174 (tp40) REVERT: B 76 ASN cc_start: 0.8392 (t0) cc_final: 0.7993 (t0) REVERT: B 169 LYS cc_start: 0.8982 (ptmm) cc_final: 0.8743 (tptp) REVERT: B 206 TYR cc_start: 0.8194 (t80) cc_final: 0.7927 (t80) REVERT: B 219 TYR cc_start: 0.7292 (t80) cc_final: 0.6653 (t80) REVERT: C 98 LEU cc_start: 0.8389 (mm) cc_final: 0.8035 (mm) REVERT: C 178 GLN cc_start: 0.8767 (pt0) cc_final: 0.8389 (pp30) REVERT: C 334 MET cc_start: 0.6630 (tpt) cc_final: 0.6424 (tpt) REVERT: D 13 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8612 (tm-30) REVERT: D 80 ARG cc_start: 0.8730 (tmm-80) cc_final: 0.8231 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2000 time to fit residues: 48.0942 Evaluate side-chains 121 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 199 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10649 Z= 0.363 Angle : 0.706 8.379 14402 Z= 0.372 Chirality : 0.045 0.179 1615 Planarity : 0.005 0.072 1768 Dihedral : 5.368 21.065 1364 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1256 helix: 0.51 (0.21), residues: 594 sheet: 0.89 (0.40), residues: 172 loop : -1.66 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 26 HIS 0.008 0.002 HIS B 213 PHE 0.027 0.002 PHE B 137 TYR 0.023 0.002 TYR D 138 ARG 0.012 0.001 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8169 (m90) cc_final: 0.7604 (m90) REVERT: B 76 ASN cc_start: 0.8448 (t0) cc_final: 0.7941 (t0) REVERT: B 87 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8554 (tm-30) REVERT: B 110 GLU cc_start: 0.8546 (tp30) cc_final: 0.8178 (tp30) REVERT: B 114 TYR cc_start: 0.8265 (t80) cc_final: 0.7690 (t80) REVERT: B 169 LYS cc_start: 0.9000 (ptmm) cc_final: 0.8788 (tptp) REVERT: B 253 LYS cc_start: 0.9276 (ptpt) cc_final: 0.9069 (ptpp) REVERT: C 178 GLN cc_start: 0.8874 (pt0) cc_final: 0.8526 (pp30) REVERT: C 199 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.6537 (m90) REVERT: C 334 MET cc_start: 0.6813 (tpt) cc_final: 0.6471 (tpt) REVERT: D 13 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8796 (tm-30) REVERT: D 110 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8514 (mm-30) REVERT: D 119 SER cc_start: 0.9284 (m) cc_final: 0.8900 (p) outliers start: 2 outliers final: 0 residues processed: 145 average time/residue: 0.1996 time to fit residues: 42.7114 Evaluate side-chains 104 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 HIS ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10649 Z= 0.166 Angle : 0.568 6.658 14402 Z= 0.297 Chirality : 0.042 0.150 1615 Planarity : 0.004 0.056 1768 Dihedral : 4.862 19.458 1364 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1256 helix: 0.83 (0.21), residues: 593 sheet: 1.16 (0.41), residues: 167 loop : -1.66 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 71 HIS 0.013 0.001 HIS C 199 PHE 0.027 0.002 PHE A 152 TYR 0.018 0.001 TYR D 138 ARG 0.008 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8642 (pttm) REVERT: A 178 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8157 (tp40) REVERT: B 76 ASN cc_start: 0.8370 (t0) cc_final: 0.7967 (t0) REVERT: B 114 TYR cc_start: 0.8247 (t80) cc_final: 0.7349 (t80) REVERT: B 169 LYS cc_start: 0.8976 (ptmm) cc_final: 0.8765 (tptp) REVERT: B 253 LYS cc_start: 0.9239 (ptpt) cc_final: 0.9030 (ptpp) REVERT: C 95 ASN cc_start: 0.8946 (t0) cc_final: 0.8743 (t0) REVERT: C 98 LEU cc_start: 0.8406 (mm) cc_final: 0.8038 (mm) REVERT: C 178 GLN cc_start: 0.8825 (pt0) cc_final: 0.8388 (pp30) REVERT: D 13 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8628 (tm-30) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1816 time to fit residues: 45.3057 Evaluate side-chains 109 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10649 Z= 0.200 Angle : 0.587 6.827 14402 Z= 0.306 Chirality : 0.043 0.179 1615 Planarity : 0.004 0.057 1768 Dihedral : 4.846 19.369 1364 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.09 % Allowed : 1.58 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1256 helix: 0.85 (0.21), residues: 595 sheet: 0.93 (0.41), residues: 173 loop : -1.50 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 26 HIS 0.009 0.001 HIS C 175 PHE 0.024 0.002 PHE A 152 TYR 0.018 0.001 TYR D 138 ARG 0.009 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9003 (ptpp) cc_final: 0.8795 (pttm) REVERT: A 178 GLN cc_start: 0.8605 (tp-100) cc_final: 0.8186 (tp40) REVERT: B 76 ASN cc_start: 0.8390 (t0) cc_final: 0.7999 (t0) REVERT: B 114 TYR cc_start: 0.8262 (t80) cc_final: 0.7239 (t80) REVERT: B 219 TYR cc_start: 0.7468 (t80) cc_final: 0.6931 (t80) REVERT: B 221 ASP cc_start: 0.7376 (p0) cc_final: 0.6970 (p0) REVERT: C 178 GLN cc_start: 0.8857 (pt0) cc_final: 0.8418 (pp30) REVERT: C 334 MET cc_start: 0.6415 (tpt) cc_final: 0.6176 (tpt) REVERT: D 13 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8628 (tm-30) REVERT: D 147 MET cc_start: 0.8892 (ppp) cc_final: 0.8576 (ppp) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1736 time to fit residues: 41.1195 Evaluate side-chains 110 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 11 optimal weight: 0.0470 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN C 187 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10649 Z= 0.354 Angle : 0.729 8.489 14402 Z= 0.383 Chirality : 0.046 0.209 1615 Planarity : 0.005 0.080 1768 Dihedral : 5.527 20.919 1364 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1256 helix: 0.35 (0.21), residues: 588 sheet: 0.79 (0.42), residues: 161 loop : -1.81 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 26 HIS 0.008 0.002 HIS C 31 PHE 0.028 0.002 PHE B 137 TYR 0.022 0.002 TYR D 138 ARG 0.012 0.001 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 ASN cc_start: 0.8409 (t0) cc_final: 0.8040 (t0) REVERT: B 113 ASN cc_start: 0.8639 (p0) cc_final: 0.8405 (p0) REVERT: B 219 TYR cc_start: 0.7327 (t80) cc_final: 0.6527 (t80) REVERT: C 131 LEU cc_start: 0.8191 (mt) cc_final: 0.7985 (mt) REVERT: C 178 GLN cc_start: 0.8946 (pt0) cc_final: 0.8473 (pp30) REVERT: C 334 MET cc_start: 0.6705 (tpt) cc_final: 0.5654 (tpt) REVERT: D 13 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8601 (tm-30) REVERT: D 71 TRP cc_start: 0.8159 (t60) cc_final: 0.7848 (t60) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1820 time to fit residues: 37.6827 Evaluate side-chains 101 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 118 optimal weight: 0.0170 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN C 175 HIS C 187 HIS ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10649 Z= 0.155 Angle : 0.601 8.428 14402 Z= 0.307 Chirality : 0.043 0.164 1615 Planarity : 0.004 0.059 1768 Dihedral : 4.819 18.954 1364 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.09 % Allowed : 0.53 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1256 helix: 0.88 (0.21), residues: 585 sheet: 0.94 (0.42), residues: 168 loop : -1.75 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 26 HIS 0.009 0.001 HIS C 175 PHE 0.028 0.001 PHE A 152 TYR 0.020 0.001 TYR B 206 ARG 0.009 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8762 (pttm) REVERT: A 178 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8187 (tp40) REVERT: B 76 ASN cc_start: 0.8308 (t0) cc_final: 0.7940 (t0) REVERT: B 114 TYR cc_start: 0.8243 (t80) cc_final: 0.7559 (t80) REVERT: B 170 GLU cc_start: 0.8924 (mp0) cc_final: 0.8335 (mp0) REVERT: B 219 TYR cc_start: 0.7311 (t80) cc_final: 0.6634 (t80) REVERT: C 95 ASN cc_start: 0.8510 (t0) cc_final: 0.8177 (t0) REVERT: C 178 GLN cc_start: 0.8835 (pt0) cc_final: 0.8389 (pp30) REVERT: C 334 MET cc_start: 0.6810 (tpt) cc_final: 0.5695 (tpt) REVERT: D 13 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8539 (tm-30) REVERT: D 71 TRP cc_start: 0.8029 (t60) cc_final: 0.7719 (t60) REVERT: D 74 PHE cc_start: 0.8425 (t80) cc_final: 0.8125 (t80) REVERT: D 80 ARG cc_start: 0.8705 (ttp-170) cc_final: 0.7574 (ttp-170) REVERT: D 82 THR cc_start: 0.8938 (m) cc_final: 0.8453 (p) REVERT: D 147 MET cc_start: 0.8994 (ppp) cc_final: 0.8520 (ppp) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1938 time to fit residues: 48.7005 Evaluate side-chains 122 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10649 Z= 0.147 Angle : 0.582 7.740 14402 Z= 0.296 Chirality : 0.043 0.176 1615 Planarity : 0.004 0.051 1768 Dihedral : 4.649 17.806 1364 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1256 helix: 1.08 (0.21), residues: 588 sheet: 1.00 (0.42), residues: 168 loop : -1.61 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 26 HIS 0.006 0.001 HIS B 213 PHE 0.024 0.001 PHE A 152 TYR 0.016 0.001 TYR B 206 ARG 0.007 0.000 ARG B 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8141 (tp40) REVERT: B 76 ASN cc_start: 0.8266 (t0) cc_final: 0.7920 (t0) REVERT: B 114 TYR cc_start: 0.8270 (t80) cc_final: 0.7432 (t80) REVERT: B 219 TYR cc_start: 0.7228 (t80) cc_final: 0.6574 (t80) REVERT: B 236 LEU cc_start: 0.9114 (tp) cc_final: 0.8879 (tp) REVERT: C 95 ASN cc_start: 0.8766 (t0) cc_final: 0.8422 (t0) REVERT: C 98 LEU cc_start: 0.8602 (mt) cc_final: 0.8344 (mt) REVERT: C 178 GLN cc_start: 0.8820 (pt0) cc_final: 0.8353 (pp30) REVERT: C 334 MET cc_start: 0.6860 (tpt) cc_final: 0.5695 (tpt) REVERT: D 13 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8521 (tm-30) REVERT: D 71 TRP cc_start: 0.8094 (t60) cc_final: 0.7697 (t60) REVERT: D 82 THR cc_start: 0.8970 (m) cc_final: 0.8492 (p) REVERT: D 119 SER cc_start: 0.9033 (m) cc_final: 0.8725 (p) REVERT: D 147 MET cc_start: 0.8974 (ppp) cc_final: 0.8698 (ppp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1945 time to fit residues: 50.0991 Evaluate side-chains 125 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 5 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: C 175 HIS C 187 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.074429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064443 restraints weight = 58970.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065970 restraints weight = 39030.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.067057 restraints weight = 28477.047| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10649 Z= 0.273 Angle : 0.662 7.882 14402 Z= 0.345 Chirality : 0.045 0.222 1615 Planarity : 0.004 0.065 1768 Dihedral : 5.067 22.099 1364 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.09 % Allowed : 0.79 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1256 helix: 0.81 (0.21), residues: 582 sheet: 0.80 (0.41), residues: 175 loop : -1.62 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 26 HIS 0.007 0.002 HIS C 175 PHE 0.032 0.002 PHE D 72 TYR 0.020 0.002 TYR D 138 ARG 0.010 0.001 ARG B 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1928.43 seconds wall clock time: 36 minutes 26.70 seconds (2186.70 seconds total)