Starting phenix.real_space_refine on Tue Sep 24 07:46:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/09_2024/8zbe_39901.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/09_2024/8zbe_39901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/09_2024/8zbe_39901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/09_2024/8zbe_39901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/09_2024/8zbe_39901.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/09_2024/8zbe_39901.cif" } resolution = 3.24 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= 0.003 sd= 0.081 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 35 5.16 5 C 4692 2.51 5 N 1325 2.21 5 O 1437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7489 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1648 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 555 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 11, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 225 Chain: "B" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1414 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 2, 'TRANS': 210} Chain breaks: 2 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 176 Chain: "D" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 329 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1602 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "P" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Chain: "C" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2443 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Time building chain proxies: 5.13, per 1000 atoms: 0.69 Number of scatterers: 7489 At special positions: 0 Unit cell: (85.6, 123.05, 120.91, 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 35 16.00 O 1437 8.00 N 1325 7.00 C 4692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 186 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied TRANS " DTR P 4 " - " PHE P 3 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTR P 4 " Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 17 sheets defined 37.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 42 through 68 removed outlier: 4.196A pdb=" N LEU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 55 " --> pdb=" O CYS A 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.751A pdb=" N ILE A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 4.022A pdb=" N PHE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.045A pdb=" N LEU A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 120 through 142 removed outlier: 3.959A pdb=" N PHE A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 4.235A pdb=" N SER A 146 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 147 " --> pdb=" O PRO A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.687A pdb=" N LYS A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Proline residue: A 173 - end of helix Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 219 through 225 removed outlier: 3.920A pdb=" N VAL A 225 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 261 removed outlier: 4.401A pdb=" N ARG A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 253 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 4.098A pdb=" N PHE A 265 " --> pdb=" O TRP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 308 removed outlier: 3.876A pdb=" N PHE A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Proline residue: A 301 - end of helix removed outlier: 3.714A pdb=" N SER A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'B' and resid 7 through 33 removed outlier: 3.912A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 removed outlier: 4.082A pdb=" N GLN B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.557A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.692A pdb=" N ASP B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 243 through 256 removed outlier: 4.316A pdb=" N MET B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.563A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 311 removed outlier: 4.133A pdb=" N CYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 352 Processing helix chain 'D' and resid 7 through 25 removed outlier: 3.574A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 3.595A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'C' and resid 4 through 26 removed outlier: 3.537A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.825A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 39 removed outlier: 6.022A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 190 removed outlier: 3.517A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP B 200 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.966A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AA6, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AA7, first strand: chain 'E' and resid 155 through 157 removed outlier: 3.681A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 157 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 176 through 179 Processing sheet with id=AA9, first strand: chain 'E' and resid 189 through 190 removed outlier: 3.501A pdb=" N TYR E 190 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.375A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.288A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.714A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 148 through 153 removed outlier: 6.713A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 148 through 153 removed outlier: 6.713A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.292A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.433A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 273 through 276 removed outlier: 6.372A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 999 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: 2.05 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1286 1.32 - 1.44: 2032 1.44 - 1.57: 4262 1.57 - 1.69: 1 1.69 - 1.81: 44 Bond restraints: 7625 Sorted by residual: bond pdb=" CD2 DTR P 4 " pdb=" CE2 DTR P 4 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.70e-02 3.46e+03 1.33e+01 bond pdb=" CA THR D 52 " pdb=" C THR D 52 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.26e-02 6.30e+03 1.07e+01 bond pdb=" C TYR E 101 " pdb=" O TYR E 101 " ideal model delta sigma weight residual 1.234 1.196 0.038 1.16e-02 7.43e+03 1.07e+01 bond pdb=" CA PHE A 201 " pdb=" C PHE A 201 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.24e-02 6.50e+03 9.94e+00 bond pdb=" N SER B 47 " pdb=" CA SER B 47 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.25e-02 6.40e+03 9.11e+00 ... (remaining 7620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 10208 2.66 - 5.31: 203 5.31 - 7.97: 32 7.97 - 10.62: 9 10.62 - 13.28: 2 Bond angle restraints: 10454 Sorted by residual: angle pdb=" N HIS A 143 " pdb=" CA HIS A 143 " pdb=" C HIS A 143 " ideal model delta sigma weight residual 108.71 121.99 -13.28 2.02e+00 2.45e-01 4.32e+01 angle pdb=" N LYS D 46 " pdb=" CA LYS D 46 " pdb=" C LYS D 46 " ideal model delta sigma weight residual 111.71 104.43 7.28 1.15e+00 7.56e-01 4.01e+01 angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 110.82 104.91 5.91 9.70e-01 1.06e+00 3.71e+01 angle pdb=" N LYS P 5 " pdb=" CA LYS P 5 " pdb=" CB LYS P 5 " ideal model delta sigma weight residual 110.50 120.47 -9.97 1.70e+00 3.46e-01 3.44e+01 angle pdb=" N LEU D 50 " pdb=" CA LEU D 50 " pdb=" C LEU D 50 " ideal model delta sigma weight residual 111.82 105.73 6.09 1.16e+00 7.43e-01 2.76e+01 ... (remaining 10449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 3921 16.51 - 33.02: 385 33.02 - 49.53: 117 49.53 - 66.04: 18 66.04 - 82.55: 6 Dihedral angle restraints: 4447 sinusoidal: 1239 harmonic: 3208 Sorted by residual: 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 93.00 138.62 -45.62 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 130.71 -37.71 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 186 " pdb=" CB CYS A 186 " ideal model delta sinusoidal sigma weight residual -86.00 -53.28 -32.72 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 4444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1057 0.063 - 0.126: 177 0.126 - 0.189: 25 0.189 - 0.251: 6 0.251 - 0.314: 1 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CA PRO E 151 " pdb=" N PRO E 151 " pdb=" C PRO E 151 " pdb=" CB PRO E 151 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA VAL D 54 " pdb=" N VAL D 54 " pdb=" C VAL D 54 " pdb=" CB VAL D 54 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE D 25 " pdb=" N ILE D 25 " pdb=" C ILE D 25 " pdb=" CB ILE D 25 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1263 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D 38 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C MET D 38 " 0.048 2.00e-02 2.50e+03 pdb=" O MET D 38 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA D 39 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 267 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C VAL A 267 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 267 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 268 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 262 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C MET C 262 " 0.040 2.00e-02 2.50e+03 pdb=" O MET C 262 " -0.015 2.00e-02 2.50e+03 pdb=" N THR C 263 " -0.013 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2373 2.81 - 3.33: 7285 3.33 - 3.85: 12510 3.85 - 4.38: 14194 4.38 - 4.90: 23743 Nonbonded interactions: 60105 Sorted by model distance: nonbonded pdb=" NH1 ARG A 137 " pdb=" OH TYR A 221 " model vdw 2.286 3.120 nonbonded pdb=" OG SER C 277 " pdb=" O LEU C 318 " model vdw 2.303 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.304 3.040 nonbonded pdb=" NE2 GLN C 220 " pdb=" O LEU C 255 " model vdw 2.317 3.120 nonbonded pdb=" O SER B 263 " pdb=" OG SER B 263 " model vdw 2.323 3.040 ... (remaining 60100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.510 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.300 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7625 Z= 0.308 Angle : 0.899 13.281 10454 Z= 0.541 Chirality : 0.051 0.314 1266 Planarity : 0.005 0.055 1370 Dihedral : 15.386 82.547 2349 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 29.24 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.25), residues: 1089 helix: -0.44 (0.28), residues: 353 sheet: -1.34 (0.38), residues: 192 loop : -2.00 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 82 HIS 0.018 0.002 HIS E 167 PHE 0.017 0.002 PHE A 264 TYR 0.026 0.002 TYR A 89 ARG 0.003 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.795 Fit side-chains REVERT: A 136 ASP cc_start: 0.6771 (t0) cc_final: 0.6565 (t0) REVERT: D 36 ASP cc_start: 0.5920 (t70) cc_final: 0.5608 (p0) REVERT: E 102 TYR cc_start: 0.7703 (p90) cc_final: 0.7389 (p90) REVERT: E 230 MET cc_start: 0.4280 (ttm) cc_final: 0.3560 (mmp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1643 time to fit residues: 24.8549 Evaluate side-chains 88 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7625 Z= 0.203 Angle : 0.589 6.530 10454 Z= 0.311 Chirality : 0.042 0.147 1266 Planarity : 0.004 0.055 1370 Dihedral : 4.733 26.258 1160 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.52 % Allowed : 26.49 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.26), residues: 1089 helix: 0.15 (0.29), residues: 355 sheet: -1.67 (0.35), residues: 217 loop : -1.61 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR E 175 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.834 Fit side-chains REVERT: C 101 MET cc_start: 0.8227 (mtt) cc_final: 0.7988 (mtt) REVERT: C 275 SER cc_start: 0.8866 (t) cc_final: 0.8633 (m) outliers start: 28 outliers final: 16 residues processed: 122 average time/residue: 0.1416 time to fit residues: 25.5119 Evaluate side-chains 110 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 310 ASN C 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7625 Z= 0.176 Angle : 0.550 7.210 10454 Z= 0.288 Chirality : 0.041 0.142 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.480 29.338 1160 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.01 % Allowed : 28.92 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 1089 helix: 0.37 (0.28), residues: 364 sheet: -1.51 (0.35), residues: 221 loop : -1.45 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.022 0.001 PHE A 264 TYR 0.024 0.001 TYR A 89 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 104 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.6058 (t80) REVERT: E 102 TYR cc_start: 0.7474 (p90) cc_final: 0.7175 (p90) outliers start: 31 outliers final: 20 residues processed: 126 average time/residue: 0.1563 time to fit residues: 28.6847 Evaluate side-chains 112 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain P residue 2 CYS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7625 Z= 0.302 Angle : 0.610 7.992 10454 Z= 0.321 Chirality : 0.043 0.146 1266 Planarity : 0.004 0.052 1370 Dihedral : 4.734 26.849 1160 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 7.27 % Allowed : 27.95 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1089 helix: 0.52 (0.28), residues: 361 sheet: -1.26 (0.36), residues: 212 loop : -1.61 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 82 HIS 0.006 0.002 HIS C 91 PHE 0.019 0.002 PHE B 199 TYR 0.024 0.002 TYR A 89 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 95 time to evaluate : 0.834 Fit side-chains REVERT: A 104 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.6165 (t80) REVERT: A 297 SER cc_start: 0.8526 (t) cc_final: 0.8138 (m) REVERT: B 23 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7430 (tt) REVERT: C 283 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.6132 (tpt90) outliers start: 45 outliers final: 31 residues processed: 128 average time/residue: 0.1723 time to fit residues: 30.9197 Evaluate side-chains 123 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain P residue 2 CYS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.0770 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 0.0010 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 overall best weight: 0.9748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7625 Z= 0.184 Angle : 0.547 8.155 10454 Z= 0.285 Chirality : 0.041 0.141 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.473 29.119 1160 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 6.79 % Allowed : 29.24 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.27), residues: 1089 helix: 0.71 (0.29), residues: 366 sheet: -1.34 (0.36), residues: 217 loop : -1.55 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.019 0.001 PHE A 264 TYR 0.026 0.001 TYR A 89 ARG 0.001 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 97 time to evaluate : 0.772 Fit side-chains REVERT: B 23 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7185 (tt) REVERT: E 102 TYR cc_start: 0.7247 (p90) cc_final: 0.6954 (p90) REVERT: C 212 ASP cc_start: 0.6816 (t70) cc_final: 0.6216 (t70) REVERT: C 297 TRP cc_start: 0.7807 (m100) cc_final: 0.7427 (m100) outliers start: 42 outliers final: 35 residues processed: 129 average time/residue: 0.1353 time to fit residues: 25.7628 Evaluate side-chains 127 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 91 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 286 TYR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain P residue 2 CYS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7625 Z= 0.172 Angle : 0.536 7.543 10454 Z= 0.279 Chirality : 0.041 0.149 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.382 33.813 1160 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 6.46 % Allowed : 29.56 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.26), residues: 1089 helix: 0.87 (0.29), residues: 366 sheet: -1.25 (0.36), residues: 208 loop : -1.53 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.019 0.001 PHE A 264 TYR 0.012 0.001 TYR E 175 ARG 0.001 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 0.852 Fit side-chains REVERT: E 102 TYR cc_start: 0.7191 (p90) cc_final: 0.6897 (p90) REVERT: C 297 TRP cc_start: 0.7775 (m100) cc_final: 0.7434 (m100) outliers start: 40 outliers final: 31 residues processed: 125 average time/residue: 0.1412 time to fit residues: 26.2270 Evaluate side-chains 122 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain P residue 2 CYS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 64 optimal weight: 0.0970 chunk 48 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7625 Z= 0.159 Angle : 0.542 8.423 10454 Z= 0.278 Chirality : 0.041 0.139 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.321 36.802 1160 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.14 % Allowed : 30.37 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.27), residues: 1089 helix: 1.10 (0.29), residues: 365 sheet: -1.21 (0.36), residues: 214 loop : -1.49 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 63 HIS 0.005 0.001 HIS C 91 PHE 0.026 0.001 PHE A 210 TYR 0.011 0.001 TYR E 175 ARG 0.002 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 100 time to evaluate : 0.830 Fit side-chains REVERT: A 205 THR cc_start: 0.4658 (m) cc_final: 0.4411 (t) REVERT: B 268 LEU cc_start: 0.5063 (mt) cc_final: 0.4836 (mt) REVERT: E 83 MET cc_start: 0.5377 (mtm) cc_final: 0.4683 (mtm) REVERT: E 102 TYR cc_start: 0.7213 (p90) cc_final: 0.6939 (p90) REVERT: C 283 ARG cc_start: 0.6217 (OUTLIER) cc_final: 0.5741 (tpt90) REVERT: C 297 TRP cc_start: 0.7785 (m100) cc_final: 0.7443 (m100) outliers start: 38 outliers final: 34 residues processed: 129 average time/residue: 0.1414 time to fit residues: 27.0882 Evaluate side-chains 133 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain P residue 2 CYS Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.0000 chunk 66 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 51 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7625 Z= 0.237 Angle : 0.575 8.129 10454 Z= 0.297 Chirality : 0.042 0.138 1266 Planarity : 0.004 0.052 1370 Dihedral : 4.492 36.333 1160 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.46 % Allowed : 30.21 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1089 helix: 1.03 (0.29), residues: 367 sheet: -1.27 (0.36), residues: 208 loop : -1.57 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.024 0.002 PHE B 199 TYR 0.016 0.002 TYR E 175 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 0.849 Fit side-chains REVERT: A 205 THR cc_start: 0.4872 (m) cc_final: 0.4625 (t) REVERT: E 102 TYR cc_start: 0.7169 (p90) cc_final: 0.6852 (p90) REVERT: P 3 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.4963 (t80) REVERT: C 283 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.6007 (tpt90) outliers start: 40 outliers final: 33 residues processed: 131 average time/residue: 0.1489 time to fit residues: 28.2404 Evaluate side-chains 131 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 96 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain P residue 2 CYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7625 Z= 0.275 Angle : 0.607 9.304 10454 Z= 0.314 Chirality : 0.043 0.145 1266 Planarity : 0.004 0.052 1370 Dihedral : 4.681 35.848 1160 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.14 % Allowed : 30.37 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 1089 helix: 0.87 (0.28), residues: 370 sheet: -1.35 (0.35), residues: 215 loop : -1.65 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 63 HIS 0.005 0.001 HIS E 232 PHE 0.023 0.002 PHE B 199 TYR 0.026 0.002 TYR A 89 ARG 0.003 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 99 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 205 THR cc_start: 0.4893 (m) cc_final: 0.4651 (t) REVERT: B 261 ASP cc_start: 0.7356 (t0) cc_final: 0.7137 (t0) REVERT: E 83 MET cc_start: 0.5376 (mtm) cc_final: 0.4658 (mtm) REVERT: E 102 TYR cc_start: 0.7414 (p90) cc_final: 0.7074 (p90) REVERT: P 3 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.5116 (t80) REVERT: C 283 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6458 (tpt90) outliers start: 38 outliers final: 35 residues processed: 129 average time/residue: 0.1440 time to fit residues: 27.4296 Evaluate side-chains 131 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain P residue 2 CYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.0050 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7625 Z= 0.255 Angle : 0.602 9.518 10454 Z= 0.311 Chirality : 0.042 0.143 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.679 39.698 1160 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 6.30 % Allowed : 30.37 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1089 helix: 0.93 (0.28), residues: 367 sheet: -1.32 (0.36), residues: 201 loop : -1.69 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 63 HIS 0.005 0.001 HIS C 91 PHE 0.022 0.002 PHE B 259 TYR 0.027 0.002 TYR A 89 ARG 0.002 0.000 ARG C 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 100 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 205 THR cc_start: 0.4762 (m) cc_final: 0.4558 (t) REVERT: E 83 MET cc_start: 0.5500 (mtm) cc_final: 0.4768 (mtm) REVERT: E 102 TYR cc_start: 0.7426 (p90) cc_final: 0.7107 (p90) REVERT: P 3 PHE cc_start: 0.5743 (OUTLIER) cc_final: 0.4950 (t80) REVERT: C 283 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6402 (tpt90) outliers start: 39 outliers final: 37 residues processed: 130 average time/residue: 0.1435 time to fit residues: 27.6111 Evaluate side-chains 137 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 98 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain P residue 2 CYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.213808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.179845 restraints weight = 10440.308| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 2.62 r_work: 0.4132 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7625 Z= 0.196 Angle : 0.566 9.549 10454 Z= 0.290 Chirality : 0.041 0.141 1266 Planarity : 0.004 0.052 1370 Dihedral : 4.526 46.759 1160 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.98 % Allowed : 30.69 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.26), residues: 1089 helix: 1.09 (0.29), residues: 364 sheet: -1.32 (0.35), residues: 210 loop : -1.57 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 63 HIS 0.005 0.001 HIS C 91 PHE 0.020 0.002 PHE A 264 TYR 0.027 0.002 TYR A 89 ARG 0.001 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.80 seconds wall clock time: 34 minutes 13.73 seconds (2053.73 seconds total)