Starting phenix.real_space_refine on Sat Aug 3 07:21:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/08_2024/8zbe_39901.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/08_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_39901/08_2024/8zbe_39901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/08_2024/8zbe_39901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/08_2024/8zbe_39901.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbe_39901/08_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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.58, per 1000 atoms: 0.61 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 - 3.50 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: 3.12 Conformation dependent library (CDL) restraints added in 1.6 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: 0.93 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: 3.32 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: 99.06 - 106.16: 187 106.16 - 113.26: 4178 113.26 - 120.36: 2715 120.36 - 127.46: 3296 127.46 - 134.56: 78 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: 3920 16.51 - 33.02: 384 33.02 - 49.53: 117 49.53 - 66.04: 17 66.04 - 82.55: 6 Dihedral angle restraints: 4444 sinusoidal: 1237 harmonic: 3207 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 4441 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: 1370 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 1367 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 1 2.04 - 2.75: 1111 2.75 - 3.47: 11041 3.47 - 4.18: 17500 4.18 - 4.90: 30456 Nonbonded interactions: 60109 Sorted by model distance: nonbonded pdb=" C PHE P 3 " pdb=" N DTR P 4 " model vdw 1.320 3.350 nonbonded pdb=" O PHE P 3 " pdb=" N DTR P 4 " model vdw 2.230 3.120 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 ... (remaining 60104 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: 0.380 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.900 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- 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 : 1.320 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 : 0.803 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: 0.1582 time to fit residues: 23.9371 Evaluate side-chains 88 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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: 0.6421 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7625 Z= 0.202 Angle : 0.589 6.476 10454 Z= 0.312 Chirality : 0.042 0.143 1266 Planarity : 0.004 0.058 1370 Dihedral : 4.743 30.809 1160 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.68 % Allowed : 26.17 % Favored : 69.14 % 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: -1.61 (0.26), residues: 1089 helix: 0.13 (0.28), residues: 362 sheet: -1.52 (0.36), residues: 209 loop : -1.70 (0.28), residues: 518 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 0.011 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 131 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.845 Fit side-chains REVERT: A 205 THR cc_start: 0.5129 (m) cc_final: 0.4846 (t) REVERT: C 101 MET cc_start: 0.8231 (mtt) cc_final: 0.7989 (mtt) REVERT: C 275 SER cc_start: 0.8871 (t) cc_final: 0.8641 (m) outliers start: 29 outliers final: 17 residues processed: 124 average time/residue: 0.1427 time to fit residues: 26.6326 Evaluate side-chains 110 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 169 ASN 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: 3.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 88 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.6390 moved from start: 0.1755 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= 0.174 Angle : 0.542 7.099 10454 Z= 0.284 Chirality : 0.041 0.141 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.396 31.461 1160 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.85 % Allowed : 28.11 % Favored : 67.04 % 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: -1.23 (0.26), residues: 1089 helix: 0.46 (0.28), residues: 364 sheet: -1.44 (0.36), residues: 219 loop : -1.43 (0.29), residues: 506 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 0.019 0.001 PHE A 264 TYR 0.026 0.001 TYR A 89 ARG 0.003 0.000 ARG C 52 *********************** 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 134 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 104 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.6067 (t80) REVERT: E 83 MET cc_start: 0.5327 (mtm) cc_final: 0.4575 (mtm) REVERT: E 102 TYR cc_start: 0.7515 (p90) cc_final: 0.7212 (p90) outliers start: 30 outliers final: 21 residues processed: 125 average time/residue: 0.1429 time to fit residues: 26.2292 Evaluate side-chains 111 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 34 MET 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: 5.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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: 0.6527 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7625 Z= 0.319 Angle : 0.621 8.334 10454 Z= 0.327 Chirality : 0.043 0.153 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.723 25.383 1160 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 7.11 % Allowed : 28.27 % Favored : 64.62 % 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: 0.54 (0.28), residues: 361 sheet: -1.27 (0.37), residues: 207 loop : -1.61 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 82 HIS 0.006 0.002 HIS C 91 PHE 0.019 0.002 PHE B 199 TYR 0.026 0.003 TYR E 175 ARG 0.003 0.000 ARG E 38 *********************** 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: 44 poor density : 96 time to evaluate : 0.722 Fit side-chains REVERT: A 104 PHE cc_start: 0.6515 (OUTLIER) cc_final: 0.6167 (t80) REVERT: A 297 SER cc_start: 0.8544 (t) cc_final: 0.8162 (m) REVERT: B 23 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7479 (tt) REVERT: C 283 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6136 (tpt90) outliers start: 44 outliers final: 31 residues processed: 129 average time/residue: 0.1552 time to fit residues: 28.5995 Evaluate side-chains 125 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 91 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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: 0.6474 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7625 Z= 0.214 Angle : 0.563 8.616 10454 Z= 0.294 Chirality : 0.041 0.143 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.515 26.278 1160 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.79 % Allowed : 29.73 % 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: -1.15 (0.26), residues: 1089 helix: 0.69 (0.29), residues: 363 sheet: -1.24 (0.36), residues: 210 loop : -1.61 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 258 HIS 0.006 0.001 HIS C 91 PHE 0.019 0.002 PHE A 264 TYR 0.026 0.002 TYR A 89 ARG 0.002 0.000 ARG E 38 *********************** 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 137 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 95 time to evaluate : 0.795 Fit side-chains REVERT: A 294 TYR cc_start: 0.8196 (m-10) cc_final: 0.7985 (m-10) REVERT: A 297 SER cc_start: 0.8531 (t) cc_final: 0.8154 (m) REVERT: B 23 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7334 (tt) REVERT: E 83 MET cc_start: 0.5600 (mtm) cc_final: 0.4547 (mtm) REVERT: C 82 TRP cc_start: 0.6514 (m-10) cc_final: 0.6210 (m-10) REVERT: C 212 ASP cc_start: 0.6883 (t70) cc_final: 0.6269 (t70) outliers start: 42 outliers final: 32 residues processed: 127 average time/residue: 0.1412 time to fit residues: 26.3861 Evaluate side-chains 125 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 D residue 54 VAL 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 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 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: 3.9990 chunk 20 optimal weight: 8.9990 chunk 61 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.6397 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7625 Z= 0.155 Angle : 0.524 7.680 10454 Z= 0.273 Chirality : 0.041 0.155 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.226 26.331 1160 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.65 % Allowed : 31.02 % 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: -0.98 (0.27), residues: 1089 helix: 0.92 (0.29), residues: 366 sheet: -1.32 (0.36), residues: 216 loop : -1.51 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.022 0.001 PHE A 264 TYR 0.028 0.001 TYR A 89 ARG 0.003 0.000 ARG E 38 *********************** 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 137 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 0.813 Fit side-chains REVERT: A 205 THR cc_start: 0.4680 (m) cc_final: 0.4425 (t) REVERT: A 210 PHE cc_start: 0.7301 (t80) cc_final: 0.7100 (t80) REVERT: E 83 MET cc_start: 0.5549 (mtm) cc_final: 0.4551 (mtm) REVERT: E 102 TYR cc_start: 0.7164 (p90) cc_final: 0.6884 (p90) REVERT: C 283 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5786 (tpt90) REVERT: C 297 TRP cc_start: 0.7772 (m100) cc_final: 0.7437 (m100) outliers start: 35 outliers final: 29 residues processed: 129 average time/residue: 0.1440 time to fit residues: 27.3658 Evaluate side-chains 122 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.6473 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7625 Z= 0.230 Angle : 0.566 8.718 10454 Z= 0.294 Chirality : 0.041 0.141 1266 Planarity : 0.004 0.052 1370 Dihedral : 4.347 23.616 1160 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 6.62 % Allowed : 30.37 % Favored : 63.00 % 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: -0.96 (0.26), residues: 1089 helix: 1.00 (0.29), residues: 367 sheet: -1.30 (0.36), residues: 208 loop : -1.56 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 63 HIS 0.005 0.001 HIS C 91 PHE 0.020 0.002 PHE B 199 TYR 0.026 0.002 TYR A 89 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: 41 poor density : 97 time to evaluate : 0.812 Fit side-chains REVERT: E 102 TYR cc_start: 0.7167 (p90) cc_final: 0.6856 (p90) REVERT: C 283 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.5967 (tpt90) REVERT: C 297 TRP cc_start: 0.7854 (m100) cc_final: 0.7460 (m100) REVERT: C 323 ASP cc_start: 0.4253 (t0) cc_final: 0.3899 (t0) outliers start: 41 outliers final: 33 residues processed: 129 average time/residue: 0.1332 time to fit residues: 25.8622 Evaluate side-chains 128 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.6502 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7625 Z= 0.261 Angle : 0.592 8.975 10454 Z= 0.307 Chirality : 0.042 0.141 1266 Planarity : 0.004 0.052 1370 Dihedral : 4.470 19.302 1160 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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: -1.02 (0.26), residues: 1089 helix: 0.94 (0.29), residues: 365 sheet: -1.31 (0.36), residues: 209 loop : -1.59 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 63 HIS 0.005 0.001 HIS C 91 PHE 0.026 0.002 PHE A 210 TYR 0.018 0.002 TYR E 175 ARG 0.002 0.000 ARG C 96 *********************** 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 137 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 0.865 Fit side-chains REVERT: E 83 MET cc_start: 0.5500 (mtm) cc_final: 0.4541 (mtm) REVERT: E 102 TYR cc_start: 0.7176 (p90) cc_final: 0.6859 (p90) REVERT: C 230 ASN cc_start: 0.6765 (OUTLIER) cc_final: 0.6503 (t0) REVERT: C 283 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.6015 (tpt90) outliers start: 37 outliers final: 34 residues processed: 128 average time/residue: 0.1374 time to fit residues: 26.5521 Evaluate side-chains 132 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL 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 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 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 230 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 chunk 76 optimal weight: 8.9990 chunk 30 optimal weight: 0.0470 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- 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: 0.6486 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7625 Z= 0.238 Angle : 0.587 9.211 10454 Z= 0.303 Chirality : 0.042 0.142 1266 Planarity : 0.004 0.053 1370 Dihedral : 4.441 18.823 1160 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % 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: 1.04 (0.29), residues: 361 sheet: -1.23 (0.36), residues: 200 loop : -1.56 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 63 HIS 0.005 0.001 HIS C 91 PHE 0.024 0.002 PHE A 210 TYR 0.016 0.002 TYR E 175 ARG 0.002 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: 40 poor density : 97 time to evaluate : 0.780 Fit side-chains REVERT: E 83 MET cc_start: 0.5499 (mtm) cc_final: 0.4555 (mtm) REVERT: E 102 TYR cc_start: 0.7176 (p90) cc_final: 0.6873 (p90) REVERT: C 230 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6564 (t0) REVERT: C 283 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.6053 (tpt90) REVERT: C 297 TRP cc_start: 0.7945 (m100) cc_final: 0.7512 (m100) outliers start: 40 outliers final: 35 residues processed: 129 average time/residue: 0.1320 time to fit residues: 25.6957 Evaluate side-chains 133 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 96 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL 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 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 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 170 ASP Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 230 ASN 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 49 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.6467 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7625 Z= 0.211 Angle : 0.580 9.416 10454 Z= 0.297 Chirality : 0.042 0.141 1266 Planarity : 0.004 0.052 1370 Dihedral : 4.380 18.165 1160 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 6.14 % Allowed : 31.02 % Favored : 62.84 % 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: -0.90 (0.26), residues: 1089 helix: 1.10 (0.29), residues: 361 sheet: -1.23 (0.36), residues: 200 loop : -1.56 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 63 HIS 0.005 0.001 HIS C 91 PHE 0.023 0.002 PHE A 210 TYR 0.028 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 134 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 0.843 Fit side-chains REVERT: E 83 MET cc_start: 0.5513 (mtm) cc_final: 0.4584 (mtm) REVERT: E 102 TYR cc_start: 0.7356 (p90) cc_final: 0.7057 (p90) REVERT: C 230 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6564 (t0) REVERT: C 283 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6082 (tpt90) REVERT: C 297 TRP cc_start: 0.7894 (m100) cc_final: 0.7469 (m100) outliers start: 38 outliers final: 35 residues processed: 126 average time/residue: 0.1421 time to fit residues: 26.3490 Evaluate side-chains 131 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL 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 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 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 170 ASP Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 230 ASN 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: 1.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4669 r_free = 0.4669 target = 0.211823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.177128 restraints weight = 10485.634| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 2.62 r_work: 0.4126 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2906 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= 0.258 Angle : 0.598 9.564 10454 Z= 0.308 Chirality : 0.042 0.143 1266 Planarity : 0.004 0.052 1370 Dihedral : 4.489 17.165 1160 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.14 % Allowed : 31.02 % Favored : 62.84 % 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: -0.97 (0.26), residues: 1089 helix: 1.08 (0.29), residues: 361 sheet: -1.27 (0.36), residues: 200 loop : -1.63 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 164 HIS 0.005 0.001 HIS C 91 PHE 0.023 0.002 PHE A 210 TYR 0.026 0.002 TYR A 89 ARG 0.002 0.000 ARG C 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1808.98 seconds wall clock time: 32 minutes 43.47 seconds (1963.47 seconds total)