Starting phenix.real_space_refine on Sat Jul 20 00:20:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/07_2024/8jii_36312_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/07_2024/8jii_36312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/07_2024/8jii_36312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/07_2024/8jii_36312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/07_2024/8jii_36312_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jii_36312/07_2024/8jii_36312_neut.cif" } resolution = 3.17 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= 0.022 sd= 0.132 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 69 5.16 5 C 5806 2.51 5 N 1543 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9083 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'IX8': 1, 'NIO': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 5.61, per 1000 atoms: 0.62 Number of scatterers: 9083 At special positions: 0 Unit cell: (93.5, 119.85, 135.15, 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 69 16.00 O 1665 8.00 N 1543 7.00 C 5806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.04 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: 3.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 32.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'B' and resid 1 through 25 removed outlier: 3.554A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.558A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 26 removed outlier: 3.835A pdb=" N GLU D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.547A pdb=" N MET D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.538A pdb=" N TRP D 211 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 215 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 216 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.551A pdb=" N ASN D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.629A pdb=" N PHE D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 4.153A pdb=" N ILE D 285 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 329 through 349 removed outlier: 3.624A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.650A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.561A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 52 removed outlier: 3.662A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.876A pdb=" N GLY A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.837A pdb=" N LEU A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.580A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 79 through 89 removed outlier: 4.258A pdb=" N LEU A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.759A pdb=" N ILE A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 4.323A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.920A pdb=" N LYS A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.516A pdb=" N GLY A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.590A pdb=" N LEU A 162 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 215 removed outlier: 3.574A pdb=" N GLU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.998A pdb=" N PHE A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.962A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 245 through 261 removed outlier: 3.741A pdb=" N VAL A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.685A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 269 through 280 removed outlier: 4.253A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.728A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.760A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.011A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.796A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.647A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.074A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.677A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.423A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190 removed outlier: 6.102A pdb=" N VAL D 34 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE D 199 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU D 36 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 4.947A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.650A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.516A pdb=" N CYS A 18 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.747A pdb=" N ILE A 169 " --> pdb=" O LEU A 176 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 927 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: 2.58 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 1275 1.25 - 1.39: 2517 1.39 - 1.53: 5075 1.53 - 1.68: 316 1.68 - 1.82: 100 Bond restraints: 9283 Sorted by residual: bond pdb=" C9 IX8 A 403 " pdb=" N10 IX8 A 403 " ideal model delta sigma weight residual 1.386 1.266 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C27 IX8 A 403 " pdb=" C32 IX8 A 403 " ideal model delta sigma weight residual 1.396 1.277 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C4 IX8 A 403 " pdb=" O5 IX8 A 403 " ideal model delta sigma weight residual 1.221 1.104 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C2 IX8 A 403 " pdb=" C25 IX8 A 403 " ideal model delta sigma weight residual 1.522 1.428 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C27 IX8 A 403 " pdb=" C28 IX8 A 403 " ideal model delta sigma weight residual 1.393 1.302 0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 9278 not shown) Histogram of bond angle deviations from ideal: 95.43 - 103.15: 62 103.15 - 110.88: 3190 110.88 - 118.60: 4060 118.60 - 126.32: 5098 126.32 - 134.04: 154 Bond angle restraints: 12564 Sorted by residual: angle pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" C VAL A 123 " ideal model delta sigma weight residual 111.90 106.74 5.16 8.10e-01 1.52e+00 4.06e+01 angle pdb=" N ILE A 77 " pdb=" CA ILE A 77 " pdb=" C ILE A 77 " ideal model delta sigma weight residual 111.62 106.70 4.92 7.90e-01 1.60e+00 3.88e+01 angle pdb=" C6 IX8 A 403 " pdb=" C4 IX8 A 403 " pdb=" N3 IX8 A 403 " ideal model delta sigma weight residual 114.73 132.05 -17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 131.62 -10.08 1.91e+00 2.74e-01 2.78e+01 angle pdb=" C23 IX8 A 403 " pdb=" C22 IX8 A 403 " pdb=" C24 IX8 A 403 " ideal model delta sigma weight residual 110.88 95.43 15.45 3.00e+00 1.11e-01 2.65e+01 ... (remaining 12559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4983 17.89 - 35.79: 470 35.79 - 53.68: 75 53.68 - 71.57: 14 71.57 - 89.46: 5 Dihedral angle restraints: 5547 sinusoidal: 2235 harmonic: 3312 Sorted by residual: dihedral pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" N PHE A 240 " pdb=" CA PHE A 240 " ideal model delta harmonic sigma weight residual 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASP A 14 " pdb=" C ASP A 14 " pdb=" N LYS A 15 " pdb=" CA LYS A 15 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C SER A 179 " pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" CB SER A 179 " ideal model delta harmonic sigma weight residual -122.60 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 5544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1010 0.047 - 0.093: 310 0.093 - 0.140: 80 0.140 - 0.186: 5 0.186 - 0.233: 3 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA GLU D 298 " pdb=" N GLU D 298 " pdb=" C GLU D 298 " pdb=" CB GLU D 298 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA CYS A 177 " pdb=" N CYS A 177 " pdb=" C CYS A 177 " pdb=" CB CYS A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA SER A 178 " pdb=" N SER A 178 " pdb=" C SER A 178 " pdb=" CB SER A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1405 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 IX8 A 403 " 0.015 2.00e-02 2.50e+03 3.10e-02 1.20e+01 pdb=" C4 IX8 A 403 " -0.060 2.00e-02 2.50e+03 pdb=" C6 IX8 A 403 " 0.029 2.00e-02 2.50e+03 pdb=" N3 IX8 A 403 " 0.002 2.00e-02 2.50e+03 pdb=" O5 IX8 A 403 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 118 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" CG ASP B 118 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP B 118 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 118 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO S 75 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.032 5.00e-02 4.00e+02 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 56 2.55 - 3.14: 6785 3.14 - 3.73: 12728 3.73 - 4.31: 18178 4.31 - 4.90: 32021 Nonbonded interactions: 69768 Sorted by model distance: nonbonded pdb=" O SER D 293 " pdb=" OD1 ASN D 294 " model vdw 1.963 3.040 nonbonded pdb=" NE2 GLN D 304 " pdb=" OE2 GLU D 308 " model vdw 2.197 2.520 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.269 2.440 nonbonded pdb=" OG SER A 62 " pdb=" OD2 ASP A 124 " model vdw 2.283 2.440 nonbonded pdb=" OE2 GLU D 8 " pdb=" OH TYR S 175 " model vdw 2.294 2.440 ... (remaining 69763 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: 1.170 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.006 0.120 9283 Z= 0.383 Angle : 0.837 17.321 12564 Z= 0.453 Chirality : 0.047 0.233 1408 Planarity : 0.004 0.058 1581 Dihedral : 14.119 89.464 3395 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.97 (0.24), residues: 1130 helix: -0.86 (0.29), residues: 325 sheet: -0.58 (0.29), residues: 301 loop : -2.01 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP S 47 HIS 0.011 0.001 HIS A 223 PHE 0.015 0.002 PHE B 234 TYR 0.028 0.002 TYR A 87 ARG 0.008 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.6785 (ttp) cc_final: 0.6464 (ttm) REVERT: D 9 ASP cc_start: 0.7642 (m-30) cc_final: 0.7297 (m-30) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2599 time to fit residues: 43.3773 Evaluate side-chains 109 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.3980 chunk 84 optimal weight: 0.0270 chunk 47 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9283 Z= 0.143 Angle : 0.563 8.048 12564 Z= 0.290 Chirality : 0.042 0.145 1408 Planarity : 0.004 0.048 1581 Dihedral : 6.179 76.798 1321 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.51 % Allowed : 5.88 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.34 (0.25), residues: 1130 helix: -0.34 (0.30), residues: 335 sheet: -0.20 (0.30), residues: 303 loop : -1.67 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE A 240 TYR 0.019 0.001 TYR A 87 ARG 0.002 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.995 Fit side-chains REVERT: D 9 ASP cc_start: 0.7621 (m-30) cc_final: 0.7279 (m-30) REVERT: D 248 LYS cc_start: 0.7259 (mptt) cc_final: 0.6986 (mmtt) REVERT: D 323 PHE cc_start: 0.7358 (m-80) cc_final: 0.7145 (m-80) REVERT: A 36 LEU cc_start: 0.7827 (mt) cc_final: 0.7627 (mp) REVERT: A 39 ILE cc_start: 0.8480 (tp) cc_final: 0.8101 (tp) REVERT: A 40 PHE cc_start: 0.7818 (m-10) cc_final: 0.7605 (m-10) outliers start: 5 outliers final: 4 residues processed: 120 average time/residue: 0.2675 time to fit residues: 42.8649 Evaluate side-chains 118 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9283 Z= 0.201 Angle : 0.559 7.355 12564 Z= 0.290 Chirality : 0.042 0.136 1408 Planarity : 0.003 0.047 1581 Dihedral : 6.034 78.181 1321 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.01 % Allowed : 9.23 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.18 (0.25), residues: 1130 helix: -0.24 (0.30), residues: 343 sheet: -0.06 (0.31), residues: 299 loop : -1.60 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.006 0.001 HIS S 35 PHE 0.015 0.001 PHE B 234 TYR 0.017 0.001 TYR S 190 ARG 0.003 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.933 Fit side-chains REVERT: D 9 ASP cc_start: 0.7656 (m-30) cc_final: 0.7318 (m-30) REVERT: D 248 LYS cc_start: 0.7282 (mptt) cc_final: 0.6956 (mmtt) REVERT: A 39 ILE cc_start: 0.8589 (tp) cc_final: 0.8202 (tp) REVERT: A 40 PHE cc_start: 0.7775 (m-80) cc_final: 0.7502 (m-10) REVERT: A 166 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7712 (tttm) outliers start: 10 outliers final: 9 residues processed: 126 average time/residue: 0.2631 time to fit residues: 43.5649 Evaluate side-chains 125 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.0270 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN A 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9283 Z= 0.196 Angle : 0.549 7.936 12564 Z= 0.285 Chirality : 0.042 0.133 1408 Planarity : 0.003 0.046 1581 Dihedral : 5.944 77.845 1321 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.42 % Allowed : 11.36 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.10 (0.25), residues: 1130 helix: -0.11 (0.30), residues: 343 sheet: -0.04 (0.31), residues: 300 loop : -1.58 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.006 0.001 HIS S 35 PHE 0.013 0.001 PHE A 240 TYR 0.016 0.001 TYR S 190 ARG 0.007 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.984 Fit side-chains REVERT: D 9 ASP cc_start: 0.7636 (m-30) cc_final: 0.7304 (m-30) REVERT: D 248 LYS cc_start: 0.7249 (mptt) cc_final: 0.6899 (mmtt) REVERT: A 40 PHE cc_start: 0.7772 (m-80) cc_final: 0.7509 (m-10) REVERT: A 92 ASP cc_start: 0.7463 (t0) cc_final: 0.7119 (t0) REVERT: A 166 LYS cc_start: 0.7893 (ttmm) cc_final: 0.7634 (tttm) REVERT: A 270 ARG cc_start: 0.7671 (ttt90) cc_final: 0.7309 (ttt-90) outliers start: 14 outliers final: 9 residues processed: 127 average time/residue: 0.2783 time to fit residues: 46.0862 Evaluate side-chains 125 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 159 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 0.0970 chunk 74 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9283 Z= 0.400 Angle : 0.674 9.857 12564 Z= 0.348 Chirality : 0.046 0.142 1408 Planarity : 0.004 0.047 1581 Dihedral : 6.419 83.403 1321 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.43 % Allowed : 12.07 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.38 (0.25), residues: 1130 helix: -0.43 (0.29), residues: 351 sheet: -0.16 (0.30), residues: 302 loop : -1.72 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 47 HIS 0.009 0.001 HIS S 35 PHE 0.019 0.002 PHE B 234 TYR 0.016 0.002 TYR S 190 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.113 Fit side-chains REVERT: D 9 ASP cc_start: 0.7662 (m-30) cc_final: 0.7313 (m-30) REVERT: S 177 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.6761 (p90) REVERT: A 136 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8820 (tt) REVERT: A 199 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7357 (mp) outliers start: 24 outliers final: 16 residues processed: 127 average time/residue: 0.2479 time to fit residues: 41.8733 Evaluate side-chains 127 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9283 Z= 0.163 Angle : 0.542 10.789 12564 Z= 0.279 Chirality : 0.041 0.136 1408 Planarity : 0.003 0.044 1581 Dihedral : 5.990 76.612 1321 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.83 % Allowed : 13.79 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.11 (0.25), residues: 1130 helix: -0.14 (0.30), residues: 346 sheet: -0.02 (0.30), residues: 300 loop : -1.60 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.016 0.001 TYR S 190 ARG 0.009 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.955 Fit side-chains REVERT: B 234 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: D 9 ASP cc_start: 0.7610 (m-30) cc_final: 0.7260 (m-30) REVERT: D 248 LYS cc_start: 0.7297 (mptt) cc_final: 0.6856 (mmtt) REVERT: S 177 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6298 (p90) REVERT: A 39 ILE cc_start: 0.8599 (tp) cc_final: 0.8217 (tp) REVERT: A 136 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 199 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7289 (mp) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 0.2432 time to fit residues: 41.2845 Evaluate side-chains 123 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.0000 chunk 91 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN A 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9283 Z= 0.131 Angle : 0.501 9.007 12564 Z= 0.260 Chirality : 0.040 0.132 1408 Planarity : 0.003 0.044 1581 Dihedral : 5.685 71.924 1321 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.01 % Allowed : 14.91 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.85 (0.25), residues: 1130 helix: 0.13 (0.31), residues: 343 sheet: 0.08 (0.30), residues: 299 loop : -1.44 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 176 HIS 0.004 0.001 HIS A 223 PHE 0.010 0.001 PHE B 199 TYR 0.017 0.001 TYR S 190 ARG 0.009 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.952 Fit side-chains REVERT: B 234 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: C 21 MET cc_start: 0.6742 (tmm) cc_final: 0.5384 (tmm) REVERT: D 9 ASP cc_start: 0.7580 (m-30) cc_final: 0.7246 (m-30) REVERT: D 243 MET cc_start: 0.7128 (mmt) cc_final: 0.6611 (mmt) REVERT: D 248 LYS cc_start: 0.7294 (mptt) cc_final: 0.6882 (mmtt) REVERT: S 177 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6015 (p90) REVERT: A 40 PHE cc_start: 0.7760 (m-80) cc_final: 0.7483 (m-10) REVERT: A 270 ARG cc_start: 0.7529 (ttt90) cc_final: 0.7259 (ttt-90) outliers start: 10 outliers final: 7 residues processed: 121 average time/residue: 0.2648 time to fit residues: 42.2713 Evaluate side-chains 117 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 159 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9283 Z= 0.160 Angle : 0.520 10.058 12564 Z= 0.267 Chirality : 0.041 0.130 1408 Planarity : 0.003 0.044 1581 Dihedral : 5.652 72.097 1321 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.13 % Allowed : 14.20 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.86 (0.25), residues: 1130 helix: 0.08 (0.30), residues: 347 sheet: 0.07 (0.30), residues: 301 loop : -1.43 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR S 190 ARG 0.008 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.945 Fit side-chains REVERT: B 234 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: C 21 MET cc_start: 0.6752 (tmm) cc_final: 0.5488 (tmm) REVERT: D 9 ASP cc_start: 0.7602 (m-30) cc_final: 0.7265 (m-30) REVERT: D 243 MET cc_start: 0.7095 (mmt) cc_final: 0.6586 (mmt) REVERT: D 248 LYS cc_start: 0.7288 (mptt) cc_final: 0.6875 (mmtt) REVERT: S 97 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8268 (p) REVERT: S 177 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.5969 (p90) REVERT: A 89 ARG cc_start: 0.7382 (ptp-110) cc_final: 0.7082 (ptp-110) REVERT: A 136 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8679 (tt) REVERT: A 270 ARG cc_start: 0.7522 (ttt90) cc_final: 0.7265 (ttt-90) outliers start: 21 outliers final: 13 residues processed: 128 average time/residue: 0.2503 time to fit residues: 42.6873 Evaluate side-chains 125 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 288 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9283 Z= 0.185 Angle : 0.535 9.303 12564 Z= 0.275 Chirality : 0.042 0.164 1408 Planarity : 0.003 0.044 1581 Dihedral : 5.696 72.854 1321 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.03 % Allowed : 14.30 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.86 (0.25), residues: 1130 helix: 0.07 (0.30), residues: 347 sheet: 0.12 (0.30), residues: 299 loop : -1.45 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.006 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR S 190 ARG 0.008 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.989 Fit side-chains REVERT: B 234 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: C 21 MET cc_start: 0.6797 (tmm) cc_final: 0.5575 (tmm) REVERT: D 9 ASP cc_start: 0.7608 (m-30) cc_final: 0.7276 (m-30) REVERT: D 243 MET cc_start: 0.7086 (mmt) cc_final: 0.6581 (mmt) REVERT: D 248 LYS cc_start: 0.7281 (mptt) cc_final: 0.6863 (mmtt) REVERT: S 177 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6108 (p90) REVERT: A 89 ARG cc_start: 0.7375 (ptp-170) cc_final: 0.7074 (ptp-110) REVERT: A 136 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8702 (tt) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.2543 time to fit residues: 43.5132 Evaluate side-chains 127 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 288 MET 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: 0.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9283 Z= 0.204 Angle : 0.556 9.672 12564 Z= 0.286 Chirality : 0.042 0.140 1408 Planarity : 0.003 0.044 1581 Dihedral : 5.751 73.873 1321 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.03 % Allowed : 14.10 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.86 (0.25), residues: 1130 helix: 0.05 (0.30), residues: 348 sheet: 0.12 (0.30), residues: 302 loop : -1.44 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.006 0.001 HIS S 35 PHE 0.012 0.001 PHE A 240 TYR 0.015 0.001 TYR S 190 ARG 0.009 0.000 ARG A 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.964 Fit side-chains REVERT: B 234 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: C 21 MET cc_start: 0.6818 (tmm) cc_final: 0.5584 (tmm) REVERT: D 9 ASP cc_start: 0.7610 (m-30) cc_final: 0.7279 (m-30) REVERT: D 248 LYS cc_start: 0.7263 (mptt) cc_final: 0.6846 (mmtt) REVERT: S 177 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6148 (p90) REVERT: A 89 ARG cc_start: 0.7378 (ptp-170) cc_final: 0.7049 (ptp-110) REVERT: A 136 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8707 (tt) outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 0.2587 time to fit residues: 42.5452 Evaluate side-chains 126 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.160247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131708 restraints weight = 12816.036| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.93 r_work: 0.3512 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9283 Z= 0.178 Angle : 0.538 9.505 12564 Z= 0.276 Chirality : 0.041 0.132 1408 Planarity : 0.003 0.044 1581 Dihedral : 5.718 73.546 1321 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.93 % Allowed : 14.50 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.82 (0.25), residues: 1130 helix: 0.09 (0.30), residues: 348 sheet: 0.15 (0.30), residues: 302 loop : -1.43 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR S 190 ARG 0.009 0.000 ARG A 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2201.05 seconds wall clock time: 39 minutes 54.28 seconds (2394.28 seconds total)