Starting phenix.real_space_refine on Wed Feb 14 02:43:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xau_33099/02_2024/7xau_33099.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xau_33099/02_2024/7xau_33099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xau_33099/02_2024/7xau_33099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xau_33099/02_2024/7xau_33099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xau_33099/02_2024/7xau_33099.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xau_33099/02_2024/7xau_33099.pdb" } resolution = 2.97 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= 0.101 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 54 5.16 5 C 5351 2.51 5 N 1437 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8443 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1923 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 12, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 178 Chain: "B" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1598 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 119 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'PEPT-D': 2} Link IDs: {'TRANS': 6} Time building chain proxies: 4.91, per 1000 atoms: 0.58 Number of scatterers: 8443 At special positions: 0 Unit cell: (87.74, 123.05, 123.05, 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 54 16.00 O 1601 8.00 N 1437 7.00 C 5351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.05 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.03 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: 3.71 Conformation dependent library (CDL) restraints added in 1.9 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN F 1 " pdb=" CB DTR F 4 " Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 32.1% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.648A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.880A pdb=" N ILE A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.820A pdb=" N ILE A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.874A pdb=" N LEU A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.824A pdb=" N MET A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.548A pdb=" N THR A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 168 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.969A pdb=" N TYR A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 removed outlier: 4.036A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.582A pdb=" N ILE A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 removed outlier: 4.131A pdb=" N ILE A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.620A pdb=" N VAL A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.625A pdb=" N SER A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 261 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.606A pdb=" N ASN A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 277 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 3.841A pdb=" N ASP A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 314 Proline residue: A 309 - end of helix removed outlier: 3.514A pdb=" N TYR A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.710A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 24 removed outlier: 3.615A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.637A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.651A pdb=" N SER B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.910A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 3.906A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 5.173A pdb=" N CYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 351 removed outlier: 4.133A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.525A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.768A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.558A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 184 removed outlier: 4.129A pdb=" N ARG A 184 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.138A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 52 removed outlier: 5.622A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 338 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.048A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.025A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.650A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 192 Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.493A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.645A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.514A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 51 removed outlier: 6.507A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.704A pdb=" N CYS E 159 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.431A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 243 " --> pdb=" O TYR E 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 190 286 hydrogen bonds defined for protein. 792 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: 2.43 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2337 1.33 - 1.46: 2330 1.46 - 1.59: 3865 1.59 - 1.71: 0 1.71 - 1.84: 74 Bond restraints: 8606 Sorted by residual: bond pdb=" CA GLU C 138 " pdb=" CB GLU C 138 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.34e-02 5.57e+03 2.48e+01 bond pdb=" C LEU A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" CG LEU C 95 " pdb=" CD1 LEU C 95 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.94e+00 bond pdb=" C THR C 243 " pdb=" N GLY C 244 " ideal model delta sigma weight residual 1.332 1.319 0.013 5.00e-03 4.00e+04 6.57e+00 bond pdb=" C CYS C 148 " pdb=" N CYS C 149 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.39e-02 5.18e+03 6.41e+00 ... (remaining 8601 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.77: 153 105.77 - 113.19: 4725 113.19 - 120.61: 3717 120.61 - 128.03: 3050 128.03 - 135.44: 75 Bond angle restraints: 11720 Sorted by residual: angle pdb=" N LYS A 73 " pdb=" CA LYS A 73 " pdb=" C LYS A 73 " ideal model delta sigma weight residual 111.71 104.67 7.04 1.34e+00 5.57e-01 2.76e+01 angle pdb=" N MET B 243 " pdb=" CA MET B 243 " pdb=" C MET B 243 " ideal model delta sigma weight residual 113.41 107.18 6.23 1.22e+00 6.72e-01 2.60e+01 angle pdb=" N ALA A 72 " pdb=" CA ALA A 72 " pdb=" C ALA A 72 " ideal model delta sigma weight residual 110.53 116.64 -6.11 1.29e+00 6.01e-01 2.24e+01 angle pdb=" N VAL B 201 " pdb=" CA VAL B 201 " pdb=" C VAL B 201 " ideal model delta sigma weight residual 106.21 111.16 -4.95 1.07e+00 8.73e-01 2.14e+01 angle pdb=" C GLN A 187 " pdb=" N TRP A 188 " pdb=" CA TRP A 188 " ideal model delta sigma weight residual 122.46 128.81 -6.35 1.41e+00 5.03e-01 2.03e+01 ... (remaining 11715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4562 17.69 - 35.38: 427 35.38 - 53.07: 68 53.07 - 70.76: 10 70.76 - 88.45: 4 Dihedral angle restraints: 5071 sinusoidal: 1767 harmonic: 3304 Sorted by residual: dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N VAL A 106 " pdb=" CA VAL A 106 " ideal model delta harmonic sigma weight residual 180.00 -134.41 -45.59 0 5.00e+00 4.00e-02 8.31e+01 dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.62 -66.62 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CA TYR A 71 " pdb=" C TYR A 71 " pdb=" N ALA A 72 " pdb=" CA ALA A 72 " ideal model delta harmonic sigma weight residual -180.00 -145.55 -34.45 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 5068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 957 0.057 - 0.113: 322 0.113 - 0.169: 80 0.169 - 0.226: 19 0.226 - 0.282: 8 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CB VAL B 218 " pdb=" CA VAL B 218 " pdb=" CG1 VAL B 218 " pdb=" CG2 VAL B 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE C 270 " pdb=" CA ILE C 270 " pdb=" CG1 ILE C 270 " pdb=" CG2 ILE C 270 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL B 339 " pdb=" CA VAL B 339 " pdb=" CG1 VAL B 339 " pdb=" CG2 VAL B 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1383 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 176 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO C 236 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 308 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 309 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.037 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 981 2.73 - 3.27: 7741 3.27 - 3.81: 14228 3.81 - 4.36: 17133 4.36 - 4.90: 29082 Nonbonded interactions: 69165 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.187 2.440 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.215 2.440 nonbonded pdb=" O THR B 260 " pdb=" OG1 THR B 316 " model vdw 2.252 2.440 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.277 2.440 ... (remaining 69160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 2.280 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.011 0.087 8606 Z= 0.714 Angle : 1.188 13.295 11720 Z= 0.694 Chirality : 0.063 0.282 1386 Planarity : 0.007 0.073 1491 Dihedral : 14.127 88.451 2925 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.17 % Allowed : 10.04 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.19), residues: 1121 helix: -4.59 (0.13), residues: 322 sheet: -1.96 (0.28), residues: 272 loop : -2.65 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 99 HIS 0.008 0.002 HIS E 167 PHE 0.037 0.004 PHE C 234 TYR 0.033 0.003 TYR C 59 ARG 0.009 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7460 (m-80) cc_final: 0.7131 (m-80) REVERT: A 75 LYS cc_start: 0.6087 (mmtm) cc_final: 0.5728 (tptt) REVERT: C 327 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7750 (m) REVERT: E 6 GLU cc_start: 0.7745 (pm20) cc_final: 0.7446 (pm20) outliers start: 10 outliers final: 4 residues processed: 204 average time/residue: 0.9546 time to fit residues: 209.9625 Evaluate side-chains 148 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 47 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 102 GLN B 188 HIS B 346 ASN C 6 GLN C 62 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8606 Z= 0.174 Angle : 0.656 11.614 11720 Z= 0.348 Chirality : 0.043 0.196 1386 Planarity : 0.005 0.049 1491 Dihedral : 6.585 44.673 1225 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.80 % Allowed : 19.14 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.69 (0.21), residues: 1121 helix: -3.37 (0.20), residues: 313 sheet: -1.44 (0.29), residues: 273 loop : -2.33 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 62 PHE 0.017 0.002 PHE C 241 TYR 0.020 0.002 TYR A 273 ARG 0.010 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8049 (mp) cc_final: 0.7779 (tt) REVERT: C 241 PHE cc_start: 0.7007 (p90) cc_final: 0.6677 (p90) REVERT: C 243 THR cc_start: 0.7906 (p) cc_final: 0.7555 (p) REVERT: E 6 GLU cc_start: 0.7655 (pm20) cc_final: 0.7209 (pm20) outliers start: 24 outliers final: 10 residues processed: 181 average time/residue: 0.8656 time to fit residues: 170.2348 Evaluate side-chains 143 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8606 Z= 0.206 Angle : 0.607 10.171 11720 Z= 0.320 Chirality : 0.042 0.162 1386 Planarity : 0.004 0.042 1491 Dihedral : 5.824 38.608 1222 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.02 % Allowed : 20.42 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.03 (0.22), residues: 1121 helix: -2.48 (0.24), residues: 314 sheet: -1.16 (0.30), residues: 262 loop : -2.10 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 241 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6725 (mtp) cc_final: 0.6462 (mtm) REVERT: B 22 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7789 (m110) REVERT: C 59 TYR cc_start: 0.7263 (m-80) cc_final: 0.6926 (m-80) REVERT: C 241 PHE cc_start: 0.6992 (p90) cc_final: 0.6683 (p90) REVERT: C 243 THR cc_start: 0.7810 (p) cc_final: 0.7480 (p) REVERT: E 6 GLU cc_start: 0.7571 (pm20) cc_final: 0.7205 (pm20) REVERT: E 19 LYS cc_start: 0.8252 (tttp) cc_final: 0.7978 (ptmm) REVERT: E 192 MET cc_start: 0.5639 (tmm) cc_final: 0.5264 (tpp) outliers start: 43 outliers final: 28 residues processed: 182 average time/residue: 0.9271 time to fit residues: 182.5642 Evaluate side-chains 165 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 53 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8606 Z= 0.229 Angle : 0.619 11.104 11720 Z= 0.321 Chirality : 0.042 0.153 1386 Planarity : 0.004 0.035 1491 Dihedral : 5.608 36.115 1222 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 6.18 % Allowed : 20.54 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.61 (0.23), residues: 1121 helix: -1.94 (0.26), residues: 320 sheet: -0.95 (0.30), residues: 270 loop : -1.93 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 334 TYR 0.012 0.001 TYR E 103 ARG 0.006 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 144 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: C 59 TYR cc_start: 0.7279 (m-80) cc_final: 0.6872 (m-80) REVERT: C 241 PHE cc_start: 0.6996 (p90) cc_final: 0.6640 (p90) REVERT: C 243 THR cc_start: 0.7833 (p) cc_final: 0.7485 (p) REVERT: E 6 GLU cc_start: 0.7553 (pm20) cc_final: 0.7167 (pm20) REVERT: E 19 LYS cc_start: 0.8268 (tttp) cc_final: 0.7987 (ptmm) REVERT: E 192 MET cc_start: 0.5412 (tmm) cc_final: 0.5180 (tpp) outliers start: 53 outliers final: 35 residues processed: 180 average time/residue: 0.9205 time to fit residues: 179.3000 Evaluate side-chains 168 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 0.0870 chunk 44 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN E 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8606 Z= 0.203 Angle : 0.604 12.602 11720 Z= 0.311 Chirality : 0.042 0.154 1386 Planarity : 0.003 0.036 1491 Dihedral : 5.385 35.803 1222 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.37 % Allowed : 22.05 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.23), residues: 1121 helix: -1.67 (0.27), residues: 328 sheet: -0.82 (0.30), residues: 260 loop : -1.86 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 PHE 0.011 0.001 PHE C 292 TYR 0.011 0.001 TYR E 103 ARG 0.008 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7241 (tm) REVERT: B 14 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6682 (tp30) REVERT: B 297 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7889 (mp0) REVERT: C 237 ASN cc_start: 0.7805 (t0) cc_final: 0.7184 (t0) REVERT: C 241 PHE cc_start: 0.6974 (p90) cc_final: 0.6623 (p90) REVERT: C 243 THR cc_start: 0.7793 (p) cc_final: 0.7459 (p) REVERT: E 6 GLU cc_start: 0.7593 (pm20) cc_final: 0.7249 (pm20) REVERT: E 19 LYS cc_start: 0.8293 (tttp) cc_final: 0.7993 (ptmm) REVERT: E 140 MET cc_start: 0.5012 (mpp) cc_final: 0.4563 (mpp) REVERT: E 153 GLU cc_start: 0.5246 (OUTLIER) cc_final: 0.3251 (pp20) outliers start: 46 outliers final: 34 residues processed: 174 average time/residue: 0.9327 time to fit residues: 175.5214 Evaluate side-chains 167 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8606 Z= 0.257 Angle : 0.632 12.489 11720 Z= 0.324 Chirality : 0.043 0.184 1386 Planarity : 0.003 0.040 1491 Dihedral : 5.409 35.094 1222 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.07 % Allowed : 22.40 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.24), residues: 1121 helix: -1.43 (0.27), residues: 325 sheet: -0.86 (0.30), residues: 271 loop : -1.74 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE C 151 TYR 0.019 0.001 TYR A 273 ARG 0.008 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 144 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7017 (tp30) REVERT: B 297 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7896 (mp0) REVERT: B 309 ASP cc_start: 0.7370 (t70) cc_final: 0.7033 (t0) REVERT: B 326 SER cc_start: 0.8859 (m) cc_final: 0.8561 (p) REVERT: C 59 TYR cc_start: 0.7240 (m-80) cc_final: 0.6694 (m-80) REVERT: C 88 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7066 (p0) REVERT: C 241 PHE cc_start: 0.7038 (p90) cc_final: 0.6694 (p90) REVERT: C 243 THR cc_start: 0.7812 (p) cc_final: 0.7491 (p) REVERT: C 290 ASP cc_start: 0.5343 (p0) cc_final: 0.5134 (p0) REVERT: E 6 GLU cc_start: 0.7548 (pm20) cc_final: 0.7217 (pm20) REVERT: E 19 LYS cc_start: 0.8292 (tttp) cc_final: 0.7984 (ptmm) REVERT: E 140 MET cc_start: 0.5180 (mpp) cc_final: 0.4685 (mpp) REVERT: E 153 GLU cc_start: 0.5307 (OUTLIER) cc_final: 0.3337 (pp20) outliers start: 52 outliers final: 39 residues processed: 183 average time/residue: 0.9071 time to fit residues: 179.7360 Evaluate side-chains 177 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 135 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 308 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8606 Z= 0.189 Angle : 0.600 12.455 11720 Z= 0.308 Chirality : 0.042 0.151 1386 Planarity : 0.003 0.040 1491 Dihedral : 5.220 34.000 1222 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.95 % Allowed : 22.64 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.24), residues: 1121 helix: -1.15 (0.28), residues: 325 sheet: -0.66 (0.30), residues: 261 loop : -1.67 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE B 334 TYR 0.010 0.001 TYR E 103 ARG 0.008 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 144 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7256 (tm) REVERT: B 14 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6981 (tp30) REVERT: B 297 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7906 (mp0) REVERT: B 309 ASP cc_start: 0.7461 (t70) cc_final: 0.7136 (t0) REVERT: B 326 SER cc_start: 0.8842 (m) cc_final: 0.8539 (p) REVERT: C 59 TYR cc_start: 0.7139 (m-80) cc_final: 0.6607 (m-80) REVERT: C 88 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.6520 (p0) REVERT: C 243 THR cc_start: 0.7799 (p) cc_final: 0.7505 (p) REVERT: E 6 GLU cc_start: 0.7550 (pm20) cc_final: 0.7247 (pm20) REVERT: E 19 LYS cc_start: 0.8281 (tttp) cc_final: 0.7972 (ptmm) REVERT: E 153 GLU cc_start: 0.5413 (OUTLIER) cc_final: 0.3409 (pp20) REVERT: E 191 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.5397 (mtp180) REVERT: E 192 MET cc_start: 0.5868 (tmm) cc_final: 0.5348 (tpp) outliers start: 51 outliers final: 34 residues processed: 181 average time/residue: 0.9232 time to fit residues: 181.1425 Evaluate side-chains 175 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 0.0570 chunk 20 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8606 Z= 0.176 Angle : 0.602 12.858 11720 Z= 0.306 Chirality : 0.042 0.144 1386 Planarity : 0.003 0.045 1491 Dihedral : 5.081 33.362 1222 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.55 % Allowed : 23.80 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1121 helix: -0.97 (0.28), residues: 332 sheet: -0.60 (0.32), residues: 246 loop : -1.64 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 PHE 0.037 0.001 PHE C 241 TYR 0.014 0.001 TYR A 273 ARG 0.010 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: B 297 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7901 (mp0) REVERT: B 309 ASP cc_start: 0.7401 (t70) cc_final: 0.7094 (t0) REVERT: B 326 SER cc_start: 0.8835 (m) cc_final: 0.8539 (p) REVERT: C 59 TYR cc_start: 0.7123 (m-80) cc_final: 0.6693 (m-80) REVERT: E 6 GLU cc_start: 0.7533 (pm20) cc_final: 0.7253 (pm20) REVERT: E 19 LYS cc_start: 0.8226 (tttp) cc_final: 0.7878 (ptmm) REVERT: E 76 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8188 (mttt) REVERT: E 153 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.3466 (pp20) REVERT: E 192 MET cc_start: 0.5697 (tmm) cc_final: 0.5287 (tpp) outliers start: 39 outliers final: 28 residues processed: 178 average time/residue: 0.9062 time to fit residues: 174.9776 Evaluate side-chains 165 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN C 75 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8606 Z= 0.268 Angle : 0.661 12.918 11720 Z= 0.335 Chirality : 0.043 0.150 1386 Planarity : 0.004 0.044 1491 Dihedral : 5.232 32.656 1222 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.55 % Allowed : 25.32 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.24), residues: 1121 helix: -0.90 (0.29), residues: 327 sheet: -0.64 (0.30), residues: 267 loop : -1.66 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.020 0.002 PHE C 292 TYR 0.012 0.001 TYR E 103 ARG 0.009 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7030 (tp30) REVERT: B 297 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7913 (mp0) REVERT: B 309 ASP cc_start: 0.7405 (t70) cc_final: 0.7094 (t0) REVERT: C 88 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7021 (p0) REVERT: E 6 GLU cc_start: 0.7573 (pm20) cc_final: 0.7272 (pm20) REVERT: E 18 ARG cc_start: 0.6333 (tpt-90) cc_final: 0.6110 (ttt90) REVERT: E 19 LYS cc_start: 0.8216 (tttp) cc_final: 0.7844 (ptmm) REVERT: E 140 MET cc_start: 0.4719 (mpp) cc_final: 0.4365 (mpp) REVERT: E 153 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.3450 (pp20) REVERT: E 192 MET cc_start: 0.6007 (tmm) cc_final: 0.5565 (tpp) outliers start: 39 outliers final: 31 residues processed: 164 average time/residue: 0.9358 time to fit residues: 166.1252 Evaluate side-chains 163 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 111 optimal weight: 0.0470 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8606 Z= 0.172 Angle : 0.627 13.368 11720 Z= 0.312 Chirality : 0.042 0.146 1386 Planarity : 0.003 0.036 1491 Dihedral : 5.015 31.535 1222 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.38 % Allowed : 26.25 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.24), residues: 1121 helix: -0.83 (0.28), residues: 344 sheet: -0.53 (0.32), residues: 246 loop : -1.61 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 99 HIS 0.002 0.001 HIS E 35 PHE 0.038 0.001 PHE C 241 TYR 0.009 0.001 TYR E 190 ARG 0.008 0.000 ARG E 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7658 (mtmt) REVERT: B 21 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7589 (ttp80) REVERT: B 297 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7917 (mp0) REVERT: B 309 ASP cc_start: 0.7397 (t70) cc_final: 0.7103 (t0) REVERT: B 326 SER cc_start: 0.8837 (m) cc_final: 0.8534 (p) REVERT: C 130 GLU cc_start: 0.7147 (mp0) cc_final: 0.6925 (mm-30) REVERT: C 214 ARG cc_start: 0.7354 (mtm180) cc_final: 0.6755 (mpp80) REVERT: E 6 GLU cc_start: 0.7514 (pm20) cc_final: 0.7231 (pm20) REVERT: E 18 ARG cc_start: 0.6398 (tpt-90) cc_final: 0.6156 (ttt90) REVERT: E 19 LYS cc_start: 0.8192 (tttp) cc_final: 0.7825 (ptmm) REVERT: E 76 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8171 (mttt) REVERT: E 138 ILE cc_start: 0.7465 (mm) cc_final: 0.7146 (mm) REVERT: E 140 MET cc_start: 0.4692 (mpp) cc_final: 0.4266 (mpp) REVERT: E 153 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.3450 (pp20) REVERT: E 192 MET cc_start: 0.5872 (tmm) cc_final: 0.5441 (tpp) outliers start: 29 outliers final: 26 residues processed: 165 average time/residue: 0.8945 time to fit residues: 160.0433 Evaluate side-chains 161 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.0010 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.0670 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 0.0020 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 overall best weight: 0.1930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.199916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.147025 restraints weight = 10610.697| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.02 r_work: 0.3626 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8606 Z= 0.141 Angle : 0.597 13.455 11720 Z= 0.298 Chirality : 0.041 0.148 1386 Planarity : 0.003 0.034 1491 Dihedral : 4.761 30.782 1222 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.22 % Allowed : 27.77 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.24), residues: 1121 helix: -0.59 (0.29), residues: 349 sheet: -0.52 (0.31), residues: 255 loop : -1.42 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS B 213 PHE 0.012 0.001 PHE B 334 TYR 0.010 0.001 TYR E 190 ARG 0.008 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3415.87 seconds wall clock time: 61 minutes 27.53 seconds (3687.53 seconds total)