Starting phenix.real_space_refine on Fri Jul 19 23:53:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/07_2024/8jiu_36328.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/07_2024/8jiu_36328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/07_2024/8jiu_36328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/07_2024/8jiu_36328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/07_2024/8jiu_36328.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/07_2024/8jiu_36328.cif" } resolution = 2.76 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= -0.000 sd= 0.019 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 57 5.16 5 C 5767 2.51 5 N 1588 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "P GLU 15": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9075 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1875 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "P" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 214 Classifications: {'peptide': 28} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2548 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3018 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 127 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.90, per 1000 atoms: 0.54 Number of scatterers: 9075 At special positions: 0 Unit cell: (78.183, 100.674, 171.36, 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 57 16.00 O 1663 8.00 N 1588 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.01 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.04 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.04 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.5 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN P 2 " Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 41.0% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 4.068A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.899A pdb=" N THR A 55 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 56' Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.584A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.697A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.582A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.624A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.962A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'P' and resid 2 through 29 No H-bonds generated for 'chain 'P' and resid 2 through 29' Processing helix chain 'B' and resid 3 through 25 removed outlier: 4.130A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.521A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 22 removed outlier: 3.662A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 4.292A pdb=" N LYS C 46 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.624A pdb=" N GLU C 58 " --> pdb=" O PRO C 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.710A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.632A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.823A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 47 removed outlier: 3.614A pdb=" N GLU R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS R 35 " --> pdb=" O PHE R 31 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 91 removed outlier: 4.312A pdb=" N HIS R 89 " --> pdb=" O PRO R 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS R 90 " --> pdb=" O TRP R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 164 removed outlier: 3.585A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 201 removed outlier: 3.784A pdb=" N ILE R 176 " --> pdb=" O THR R 172 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU R 197 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 216 Processing helix chain 'R' and resid 220 through 252 removed outlier: 3.700A pdb=" N GLY R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 271 Processing helix chain 'R' and resid 272 through 289 removed outlier: 4.371A pdb=" N MET R 276 " --> pdb=" O TRP R 272 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 307 removed outlier: 4.355A pdb=" N ILE R 306 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 336 removed outlier: 4.077A pdb=" N ASN R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA R 331 " --> pdb=" O GLN R 327 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG R 336 " --> pdb=" O LYS R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 353 removed outlier: 4.161A pdb=" N LEU R 347 " --> pdb=" O TYR R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 354 through 358 removed outlier: 4.055A pdb=" N LEU R 357 " --> pdb=" O LEU R 354 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU R 358 " --> pdb=" O ILE R 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 354 through 358' Processing helix chain 'R' and resid 360 through 365 Processing helix chain 'R' and resid 374 through 402 removed outlier: 3.545A pdb=" N ARG R 378 " --> pdb=" O GLN R 374 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.564A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.675A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.660A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.720A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.295A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.945A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.416A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.717A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.593A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.917A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1137 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: 2.71 Time building geometry restraints manager: 3.94 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: 1749 1.32 - 1.45: 2511 1.45 - 1.57: 4931 1.57 - 1.70: 2 1.70 - 1.82: 78 Bond restraints: 9271 Sorted by residual: bond pdb=" CA PHE R 365 " pdb=" C PHE R 365 " ideal model delta sigma weight residual 1.533 1.493 0.040 5.60e-03 3.19e+04 5.19e+01 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.371 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " ideal model delta sigma weight residual 1.538 1.623 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" N ARG R 94 " pdb=" CA ARG R 94 " ideal model delta sigma weight residual 1.455 1.505 -0.050 1.23e-02 6.61e+03 1.64e+01 bond pdb=" CA THR N 111 " pdb=" C THR N 111 " ideal model delta sigma weight residual 1.523 1.475 0.047 1.28e-02 6.10e+03 1.37e+01 ... (remaining 9266 not shown) Histogram of bond angle deviations from ideal: 93.65 - 102.48: 36 102.48 - 111.31: 3885 111.31 - 120.15: 4630 120.15 - 128.98: 3940 128.98 - 137.81: 89 Bond angle restraints: 12580 Sorted by residual: angle pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 118.04 93.65 24.39 3.00e+00 1.11e-01 6.61e+01 angle pdb=" N LEU B 30 " pdb=" CA LEU B 30 " pdb=" C LEU B 30 " ideal model delta sigma weight residual 113.43 104.11 9.32 1.26e+00 6.30e-01 5.47e+01 angle pdb=" N LEU R 47 " pdb=" CA LEU R 47 " pdb=" C LEU R 47 " ideal model delta sigma weight residual 112.23 102.92 9.31 1.26e+00 6.30e-01 5.46e+01 angle pdb=" N VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta sigma weight residual 110.50 115.02 -4.52 6.30e-01 2.52e+00 5.15e+01 angle pdb=" N GLY R 196 " pdb=" CA GLY R 196 " pdb=" C GLY R 196 " ideal model delta sigma weight residual 112.50 104.46 8.04 1.16e+00 7.43e-01 4.81e+01 ... (remaining 12575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4708 17.30 - 34.60: 472 34.60 - 51.90: 208 51.90 - 69.20: 67 69.20 - 86.50: 16 Dihedral angle restraints: 5471 sinusoidal: 2062 harmonic: 3409 Sorted by residual: dihedral pdb=" C VAL R 280 " pdb=" N VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta harmonic sigma weight residual -122.00 -138.87 16.87 0 2.50e+00 1.60e-01 4.56e+01 dihedral pdb=" N VAL R 280 " pdb=" C VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta harmonic sigma weight residual 123.40 138.75 -15.35 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 67 " pdb=" CB CYS R 67 " ideal model delta sinusoidal sigma weight residual -86.00 -39.94 -46.06 1 1.00e+01 1.00e-02 2.94e+01 ... (remaining 5468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1300 0.119 - 0.238: 93 0.238 - 0.357: 12 0.357 - 0.476: 3 0.476 - 0.595: 4 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA VAL R 280 " pdb=" N VAL R 280 " pdb=" C VAL R 280 " pdb=" CB VAL R 280 " both_signs ideal model delta sigma weight residual False 2.44 1.85 0.59 2.00e-01 2.50e+01 8.85e+00 chirality pdb=" CG LEU R 85 " pdb=" CB LEU R 85 " pdb=" CD1 LEU R 85 " pdb=" CD2 LEU R 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.82e+00 ... (remaining 1409 not shown) Planarity restraints: 1609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 52 " -0.027 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR C 52 " 0.094 2.00e-02 2.50e+03 pdb=" O THR C 52 " -0.036 2.00e-02 2.50e+03 pdb=" N PRO C 53 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " 0.018 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" C04 D6M P 101 " -0.038 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " -0.031 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " 0.047 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA DSN P 2 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C DSN P 2 " -0.058 2.00e-02 2.50e+03 pdb=" O DSN P 2 " 0.022 2.00e-02 2.50e+03 pdb=" N GLN P 3 " 0.019 2.00e-02 2.50e+03 ... (remaining 1606 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 1 2.09 - 2.79: 2532 2.79 - 3.49: 12392 3.49 - 4.20: 21749 4.20 - 4.90: 37135 Nonbonded interactions: 73809 Sorted by model distance: nonbonded pdb=" C HIS P 1 " pdb=" N DSN P 2 " model vdw 1.382 3.350 nonbonded pdb=" N GLN R 120 " pdb=" OE1 GLN R 120 " model vdw 2.217 2.520 nonbonded pdb=" O SER R 203 " pdb=" OG SER R 203 " model vdw 2.254 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.265 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.311 2.440 ... (remaining 73804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.790 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.008 0.124 9271 Z= 0.491 Angle : 1.138 24.390 12580 Z= 0.729 Chirality : 0.075 0.595 1412 Planarity : 0.006 0.080 1609 Dihedral : 18.355 86.500 3249 Min Nonbonded Distance : 1.382 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 1.29 % Allowed : 6.38 % Favored : 92.33 % Rotamer: Outliers : 15.73 % Allowed : 7.54 % Favored : 76.72 % Cbeta Deviations : 0.36 % 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: -2.62 (0.23), residues: 1160 helix: -1.51 (0.24), residues: 437 sheet: -1.35 (0.35), residues: 211 loop : -1.99 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 241 HIS 0.007 0.001 HIS B 91 PHE 0.024 0.002 PHE N 68 TYR 0.019 0.001 TYR R 145 ARG 0.008 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 193 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8272 (mm-30) REVERT: A 294 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: P 21 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8074 (t0) REVERT: P 25 TRP cc_start: 0.8655 (t60) cc_final: 0.7569 (t60) REVERT: B 10 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.9017 (mm-30) REVERT: B 17 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8708 (tm-30) REVERT: B 251 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8557 (mtt90) REVERT: B 259 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: B 301 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8034 (mmmm) REVERT: C 17 GLU cc_start: 0.9309 (tp30) cc_final: 0.8584 (tm-30) REVERT: C 21 MET cc_start: 0.9221 (mmp) cc_final: 0.9009 (mmm) REVERT: C 26 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8431 (p0) REVERT: C 28 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8317 (pp) REVERT: C 32 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8242 (tppt) REVERT: N 18 LEU cc_start: 0.8435 (mt) cc_final: 0.8176 (mt) REVERT: N 28 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8395 (p) REVERT: N 73 ASP cc_start: 0.8249 (t70) cc_final: 0.7858 (t0) REVERT: R 28 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8095 (m) REVERT: R 30 ASP cc_start: 0.9594 (OUTLIER) cc_final: 0.9256 (p0) REVERT: R 39 TYR cc_start: 0.8495 (t80) cc_final: 0.8155 (t80) REVERT: R 88 HIS cc_start: 0.7919 (t-90) cc_final: 0.7692 (t-90) REVERT: R 123 MET cc_start: 0.7428 (mmt) cc_final: 0.7005 (mmm) REVERT: R 144 MET cc_start: 0.9261 (tmm) cc_final: 0.8503 (tmm) REVERT: R 145 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8013 (p90) REVERT: R 201 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7789 (ttt90) REVERT: R 211 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8993 (p) REVERT: R 231 MET cc_start: 0.9036 (ttp) cc_final: 0.8581 (ttp) REVERT: R 251 ASN cc_start: 0.8744 (t0) cc_final: 0.8120 (t0) REVERT: R 287 CYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8813 (t) REVERT: R 293 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: R 368 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8560 (t) REVERT: R 385 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8251 (t0) REVERT: R 405 LYS cc_start: 0.9022 (mmpt) cc_final: 0.8616 (mmmt) outliers start: 146 outliers final: 21 residues processed: 287 average time/residue: 1.1413 time to fit residues: 349.2755 Evaluate side-chains 189 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 58 CYS Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 201 ARG Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 GLN Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN C 18 GLN R 46 ASN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9271 Z= 0.196 Angle : 0.657 10.139 12580 Z= 0.342 Chirality : 0.042 0.297 1412 Planarity : 0.005 0.070 1609 Dihedral : 9.974 102.056 1372 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.60 % Favored : 94.05 % Rotamer: Outliers : 4.53 % Allowed : 19.50 % Favored : 75.97 % 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: -1.50 (0.24), residues: 1160 helix: -0.15 (0.25), residues: 444 sheet: -0.95 (0.34), residues: 220 loop : -1.74 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.007 0.001 HIS R 45 PHE 0.010 0.001 PHE R 97 TYR 0.023 0.001 TYR R 145 ARG 0.009 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8341 (mm-30) REVERT: A 228 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7742 (mtp85) REVERT: A 294 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: P 21 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7891 (t0) REVERT: P 26 LEU cc_start: 0.9423 (tp) cc_final: 0.8749 (tp) REVERT: B 12 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8790 (pp20) REVERT: B 17 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8770 (tm-30) REVERT: B 325 MET cc_start: 0.8629 (tpt) cc_final: 0.8422 (tpp) REVERT: C 17 GLU cc_start: 0.9285 (tp30) cc_final: 0.8565 (tp30) REVERT: C 21 MET cc_start: 0.9007 (mmp) cc_final: 0.8546 (mmm) REVERT: C 28 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8409 (pp) REVERT: C 32 LYS cc_start: 0.8953 (tptp) cc_final: 0.8280 (tppt) REVERT: C 42 GLU cc_start: 0.8698 (pp20) cc_final: 0.8385 (pm20) REVERT: C 44 HIS cc_start: 0.6279 (OUTLIER) cc_final: 0.6016 (p-80) REVERT: C 48 ASP cc_start: 0.8593 (t0) cc_final: 0.8377 (t0) REVERT: N 73 ASP cc_start: 0.8188 (t70) cc_final: 0.7637 (t0) REVERT: R 28 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8115 (m) REVERT: R 29 MET cc_start: 0.8152 (tpt) cc_final: 0.7613 (tpt) REVERT: R 31 PHE cc_start: 0.9351 (m-80) cc_final: 0.9076 (m-80) REVERT: R 39 TYR cc_start: 0.8476 (t80) cc_final: 0.8130 (t80) REVERT: R 108 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8846 (mmp80) REVERT: R 127 GLU cc_start: 0.8608 (pm20) cc_final: 0.8408 (pm20) REVERT: R 170 HIS cc_start: 0.5672 (OUTLIER) cc_final: 0.4563 (t70) REVERT: R 231 MET cc_start: 0.8978 (ttp) cc_final: 0.8626 (ttp) REVERT: R 405 LYS cc_start: 0.9023 (mmpt) cc_final: 0.8592 (mmmt) outliers start: 42 outliers final: 17 residues processed: 184 average time/residue: 1.2070 time to fit residues: 236.9448 Evaluate side-chains 168 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.0270 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN N 120 GLN R 45 HIS ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9271 Z= 0.196 Angle : 0.604 8.340 12580 Z= 0.313 Chirality : 0.041 0.300 1412 Planarity : 0.004 0.061 1609 Dihedral : 7.673 84.853 1326 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.22 % Favored : 95.43 % Rotamer: Outliers : 4.42 % Allowed : 21.55 % Favored : 74.03 % 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 (0.25), residues: 1160 helix: 0.43 (0.26), residues: 450 sheet: -0.68 (0.34), residues: 217 loop : -1.64 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 115 HIS 0.010 0.001 HIS R 44 PHE 0.013 0.001 PHE R 33 TYR 0.022 0.001 TYR R 145 ARG 0.008 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8305 (mm-30) REVERT: A 228 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7838 (mtp85) REVERT: A 294 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: P 26 LEU cc_start: 0.9406 (tp) cc_final: 0.9079 (tp) REVERT: B 10 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9179 (tp30) REVERT: B 12 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8875 (pp20) REVERT: B 45 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8504 (mtt) REVERT: B 301 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8188 (mmmm) REVERT: C 17 GLU cc_start: 0.9301 (tp30) cc_final: 0.8093 (tp30) REVERT: C 21 MET cc_start: 0.9110 (mmp) cc_final: 0.8728 (mmm) REVERT: C 28 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8351 (pp) REVERT: C 32 LYS cc_start: 0.8980 (tptp) cc_final: 0.8403 (tppt) REVERT: C 42 GLU cc_start: 0.8715 (pp20) cc_final: 0.8358 (pm20) REVERT: C 44 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.6106 (p-80) REVERT: C 48 ASP cc_start: 0.8615 (t0) cc_final: 0.8321 (t0) REVERT: N 73 ASP cc_start: 0.8275 (t70) cc_final: 0.7639 (t0) REVERT: N 83 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7681 (mtt) REVERT: R 31 PHE cc_start: 0.9505 (m-80) cc_final: 0.9073 (m-80) REVERT: R 39 TYR cc_start: 0.8630 (t80) cc_final: 0.8356 (t80) REVERT: R 115 TRP cc_start: 0.7230 (p-90) cc_final: 0.6960 (p-90) REVERT: R 127 GLU cc_start: 0.8679 (pm20) cc_final: 0.8447 (pm20) REVERT: R 170 HIS cc_start: 0.5898 (OUTLIER) cc_final: 0.4812 (t70) REVERT: R 231 MET cc_start: 0.8931 (ttp) cc_final: 0.8573 (ttp) REVERT: R 405 LYS cc_start: 0.9079 (mmpt) cc_final: 0.8647 (mmmt) outliers start: 41 outliers final: 19 residues processed: 172 average time/residue: 1.2216 time to fit residues: 224.1606 Evaluate side-chains 162 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain P residue 1 HIS Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9271 Z= 0.200 Angle : 0.604 9.896 12580 Z= 0.310 Chirality : 0.041 0.275 1412 Planarity : 0.004 0.057 1609 Dihedral : 6.446 86.532 1311 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.74 % Favored : 95.00 % Rotamer: Outliers : 3.66 % Allowed : 23.60 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1160 helix: 0.68 (0.26), residues: 450 sheet: -0.47 (0.34), residues: 217 loop : -1.43 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 36 HIS 0.017 0.001 HIS R 44 PHE 0.011 0.001 PHE R 95 TYR 0.022 0.001 TYR R 145 ARG 0.008 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7913 (mtp85) REVERT: A 292 ASN cc_start: 0.8897 (t0) cc_final: 0.8671 (t0) REVERT: A 294 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: B 9 GLN cc_start: 0.9512 (mp10) cc_final: 0.9219 (mp10) REVERT: B 10 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9164 (tp30) REVERT: B 12 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8867 (pp20) REVERT: B 45 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8498 (mtt) REVERT: B 301 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8367 (mmmm) REVERT: C 21 MET cc_start: 0.8967 (mmp) cc_final: 0.8660 (mmm) REVERT: C 28 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8283 (pp) REVERT: C 32 LYS cc_start: 0.8960 (tptp) cc_final: 0.8381 (tppt) REVERT: C 48 ASP cc_start: 0.8699 (t0) cc_final: 0.8335 (t0) REVERT: N 73 ASP cc_start: 0.8265 (t70) cc_final: 0.7589 (t0) REVERT: R 39 TYR cc_start: 0.8900 (t80) cc_final: 0.8411 (t80) REVERT: R 115 TRP cc_start: 0.7236 (p-90) cc_final: 0.6866 (p-90) REVERT: R 127 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: R 136 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8828 (mtpp) REVERT: R 170 HIS cc_start: 0.5917 (OUTLIER) cc_final: 0.4828 (t70) REVERT: R 231 MET cc_start: 0.8842 (ttp) cc_final: 0.8586 (ttp) REVERT: R 385 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8544 (m-30) REVERT: R 405 LYS cc_start: 0.9107 (mmpt) cc_final: 0.8653 (mmmt) outliers start: 34 outliers final: 16 residues processed: 169 average time/residue: 1.1924 time to fit residues: 215.1963 Evaluate side-chains 161 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain P residue 1 HIS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 124 ASP Chi-restraints excluded: chain R residue 127 GLU Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 385 ASP Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 16 ASN B 88 ASN C 18 GLN N 120 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN R 177 HIS ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 9271 Z= 0.442 Angle : 0.707 9.034 12580 Z= 0.365 Chirality : 0.045 0.265 1412 Planarity : 0.005 0.056 1609 Dihedral : 6.616 79.668 1309 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.26 % Favored : 94.48 % Rotamer: Outliers : 4.63 % Allowed : 24.03 % Favored : 71.34 % 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: -0.68 (0.25), residues: 1160 helix: 0.63 (0.26), residues: 455 sheet: -0.41 (0.33), residues: 221 loop : -1.48 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 36 HIS 0.020 0.003 HIS R 44 PHE 0.018 0.002 PHE N 108 TYR 0.025 0.002 TYR R 145 ARG 0.014 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8054 (mtp85) REVERT: B 9 GLN cc_start: 0.9543 (mp10) cc_final: 0.9230 (mp10) REVERT: B 10 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9158 (tp30) REVERT: B 12 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8827 (pp20) REVERT: B 45 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8621 (mtt) REVERT: C 17 GLU cc_start: 0.9337 (tp30) cc_final: 0.8939 (mm-30) REVERT: C 21 MET cc_start: 0.8974 (mmp) cc_final: 0.8682 (mmm) REVERT: C 28 ILE cc_start: 0.8794 (mm) cc_final: 0.8202 (pp) REVERT: C 32 LYS cc_start: 0.8923 (tptp) cc_final: 0.8363 (tppt) REVERT: C 42 GLU cc_start: 0.8749 (pp20) cc_final: 0.8444 (pm20) REVERT: C 48 ASP cc_start: 0.8916 (t0) cc_final: 0.8486 (t0) REVERT: N 73 ASP cc_start: 0.8310 (t70) cc_final: 0.7661 (t0) REVERT: R 39 TYR cc_start: 0.9022 (t80) cc_final: 0.8507 (t80) REVERT: R 115 TRP cc_start: 0.7482 (p-90) cc_final: 0.7077 (p-90) REVERT: R 127 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: R 136 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8876 (mtpp) REVERT: R 231 MET cc_start: 0.9009 (ttp) cc_final: 0.8765 (ttp) REVERT: R 245 GLU cc_start: 0.8592 (tp30) cc_final: 0.8313 (tp30) REVERT: R 385 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8605 (m-30) REVERT: R 405 LYS cc_start: 0.9175 (mmpt) cc_final: 0.8762 (mmmt) outliers start: 43 outliers final: 25 residues processed: 169 average time/residue: 1.1074 time to fit residues: 200.4207 Evaluate side-chains 162 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 127 GLU Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 215 TRP Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 385 ASP Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9271 Z= 0.199 Angle : 0.640 10.337 12580 Z= 0.322 Chirality : 0.041 0.241 1412 Planarity : 0.004 0.056 1609 Dihedral : 5.930 59.758 1304 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.48 % Favored : 95.26 % Rotamer: Outliers : 3.12 % Allowed : 26.29 % Favored : 70.58 % 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: -0.42 (0.25), residues: 1160 helix: 0.82 (0.26), residues: 461 sheet: -0.25 (0.34), residues: 220 loop : -1.34 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 36 HIS 0.019 0.001 HIS R 44 PHE 0.009 0.001 PHE B 151 TYR 0.020 0.001 TYR R 145 ARG 0.010 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8036 (mtp85) REVERT: A 386 MET cc_start: 0.8948 (ttp) cc_final: 0.8711 (ttp) REVERT: P 21 ASP cc_start: 0.7941 (t0) cc_final: 0.6962 (t0) REVERT: B 9 GLN cc_start: 0.9542 (mp10) cc_final: 0.9231 (mp10) REVERT: B 10 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9136 (tp30) REVERT: B 12 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8842 (pp20) REVERT: B 301 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8417 (mmmm) REVERT: C 17 GLU cc_start: 0.9315 (tp30) cc_final: 0.8935 (tp30) REVERT: C 28 ILE cc_start: 0.8859 (mm) cc_final: 0.8384 (pp) REVERT: C 32 LYS cc_start: 0.8954 (tptp) cc_final: 0.8380 (tppt) REVERT: C 46 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8743 (pptt) REVERT: C 48 ASP cc_start: 0.8776 (t0) cc_final: 0.8303 (t0) REVERT: N 73 ASP cc_start: 0.8347 (t70) cc_final: 0.7743 (t0) REVERT: R 39 TYR cc_start: 0.8970 (t80) cc_final: 0.8474 (t80) REVERT: R 127 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: R 136 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8880 (mtpp) REVERT: R 328 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8607 (tp) REVERT: R 405 LYS cc_start: 0.9145 (mmpt) cc_final: 0.8799 (mmpt) outliers start: 29 outliers final: 14 residues processed: 161 average time/residue: 1.1707 time to fit residues: 201.4803 Evaluate side-chains 152 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 127 GLU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 368 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 9271 Z= 0.196 Angle : 0.659 12.741 12580 Z= 0.325 Chirality : 0.041 0.229 1412 Planarity : 0.004 0.055 1609 Dihedral : 5.563 50.540 1304 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.91 % Favored : 94.83 % Rotamer: Outliers : 3.02 % Allowed : 27.37 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.30 (0.25), residues: 1160 helix: 0.95 (0.26), residues: 462 sheet: -0.20 (0.34), residues: 214 loop : -1.31 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 115 HIS 0.019 0.001 HIS R 44 PHE 0.009 0.001 PHE R 391 TYR 0.020 0.001 TYR R 145 ARG 0.012 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8055 (mtp85) REVERT: P 21 ASP cc_start: 0.7852 (t0) cc_final: 0.6715 (t0) REVERT: B 9 GLN cc_start: 0.9535 (mp10) cc_final: 0.9206 (mp10) REVERT: B 10 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9177 (tp30) REVERT: B 12 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8825 (pp20) REVERT: B 301 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8400 (mmmm) REVERT: C 20 LYS cc_start: 0.8868 (ptpt) cc_final: 0.8419 (ptpp) REVERT: C 28 ILE cc_start: 0.8895 (mm) cc_final: 0.8564 (pp) REVERT: C 46 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8681 (pptt) REVERT: C 48 ASP cc_start: 0.8695 (t0) cc_final: 0.8180 (t0) REVERT: N 73 ASP cc_start: 0.8352 (t70) cc_final: 0.7739 (t0) REVERT: R 31 PHE cc_start: 0.9661 (m-80) cc_final: 0.9273 (m-80) REVERT: R 39 TYR cc_start: 0.8968 (t80) cc_final: 0.8404 (t80) REVERT: R 115 TRP cc_start: 0.7059 (p-90) cc_final: 0.6768 (p-90) REVERT: R 136 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8903 (mtpp) REVERT: R 328 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8647 (tp) REVERT: R 385 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8606 (m-30) outliers start: 28 outliers final: 15 residues processed: 160 average time/residue: 1.1204 time to fit residues: 192.0409 Evaluate side-chains 156 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 0.0980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9271 Z= 0.198 Angle : 0.663 11.791 12580 Z= 0.328 Chirality : 0.041 0.222 1412 Planarity : 0.004 0.056 1609 Dihedral : 5.465 50.081 1304 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.57 % Favored : 95.17 % Rotamer: Outliers : 2.37 % Allowed : 28.88 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.24 (0.25), residues: 1160 helix: 0.96 (0.26), residues: 464 sheet: -0.17 (0.34), residues: 212 loop : -1.22 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 241 HIS 0.008 0.001 HIS R 45 PHE 0.008 0.001 PHE B 151 TYR 0.018 0.001 TYR R 145 ARG 0.012 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8062 (mtp85) REVERT: P 21 ASP cc_start: 0.7762 (t0) cc_final: 0.6908 (t0) REVERT: B 9 GLN cc_start: 0.9562 (mp10) cc_final: 0.9217 (mp10) REVERT: B 10 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9166 (tp30) REVERT: B 12 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8799 (pp20) REVERT: B 301 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8386 (mmmm) REVERT: C 28 ILE cc_start: 0.8868 (mm) cc_final: 0.8571 (pp) REVERT: C 48 ASP cc_start: 0.8657 (t0) cc_final: 0.7580 (t0) REVERT: N 73 ASP cc_start: 0.8339 (t70) cc_final: 0.7739 (t0) REVERT: R 30 ASP cc_start: 0.9619 (p0) cc_final: 0.9300 (p0) REVERT: R 31 PHE cc_start: 0.9662 (m-80) cc_final: 0.9090 (m-10) REVERT: R 39 TYR cc_start: 0.8983 (t80) cc_final: 0.8364 (t80) REVERT: R 136 LYS cc_start: 0.9183 (mtpt) cc_final: 0.8878 (mtpp) REVERT: R 231 MET cc_start: 0.8928 (ttp) cc_final: 0.8659 (ttp) REVERT: R 328 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8697 (tp) REVERT: R 385 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8345 (m-30) outliers start: 22 outliers final: 15 residues processed: 158 average time/residue: 1.1605 time to fit residues: 196.3873 Evaluate side-chains 154 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 9271 Z= 0.331 Angle : 0.721 14.182 12580 Z= 0.360 Chirality : 0.043 0.218 1412 Planarity : 0.005 0.060 1609 Dihedral : 5.672 47.221 1304 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.83 % Favored : 94.83 % Rotamer: Outliers : 2.48 % Allowed : 29.53 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.16 (0.25), residues: 1160 helix: 1.02 (0.26), residues: 458 sheet: -0.03 (0.34), residues: 216 loop : -1.20 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 115 HIS 0.028 0.002 HIS R 45 PHE 0.026 0.002 PHE P 22 TYR 0.021 0.002 TYR R 145 ARG 0.012 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8111 (mtp85) REVERT: P 22 PHE cc_start: 0.8939 (t80) cc_final: 0.8716 (t80) REVERT: B 9 GLN cc_start: 0.9560 (mp10) cc_final: 0.9214 (mp10) REVERT: B 10 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9189 (tp30) REVERT: B 12 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8769 (pp20) REVERT: B 45 MET cc_start: 0.9159 (mmm) cc_final: 0.8506 (mtt) REVERT: B 301 LYS cc_start: 0.8749 (mmmm) cc_final: 0.8513 (mmmm) REVERT: C 17 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8934 (mm-30) REVERT: C 26 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8325 (p0) REVERT: N 73 ASP cc_start: 0.8316 (t70) cc_final: 0.7677 (t0) REVERT: R 31 PHE cc_start: 0.9653 (m-80) cc_final: 0.9167 (m-80) REVERT: R 39 TYR cc_start: 0.9010 (t80) cc_final: 0.8377 (t80) REVERT: R 136 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8872 (mtpp) REVERT: R 231 MET cc_start: 0.8994 (ttp) cc_final: 0.8777 (ttp) REVERT: R 385 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8372 (m-30) outliers start: 23 outliers final: 14 residues processed: 151 average time/residue: 1.1870 time to fit residues: 191.6437 Evaluate side-chains 149 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9271 Z= 0.211 Angle : 0.715 12.525 12580 Z= 0.357 Chirality : 0.042 0.217 1412 Planarity : 0.005 0.064 1609 Dihedral : 5.560 48.029 1304 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.31 % Favored : 95.34 % Rotamer: Outliers : 2.16 % Allowed : 30.17 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.09 (0.25), residues: 1160 helix: 1.02 (0.26), residues: 458 sheet: 0.06 (0.35), residues: 215 loop : -1.14 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 115 HIS 0.012 0.001 HIS R 45 PHE 0.027 0.001 PHE P 22 TYR 0.018 0.001 TYR R 145 ARG 0.014 0.001 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8108 (mtp85) REVERT: B 9 GLN cc_start: 0.9565 (mp10) cc_final: 0.9231 (mp10) REVERT: B 12 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8791 (pp20) REVERT: B 260 GLU cc_start: 0.8522 (pt0) cc_final: 0.7847 (tt0) REVERT: B 301 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8525 (mmmm) REVERT: C 42 GLU cc_start: 0.8741 (pp20) cc_final: 0.8443 (pm20) REVERT: N 73 ASP cc_start: 0.8283 (t70) cc_final: 0.7677 (t0) REVERT: R 30 ASP cc_start: 0.9565 (p0) cc_final: 0.9327 (p0) REVERT: R 31 PHE cc_start: 0.9624 (m-80) cc_final: 0.9126 (m-80) REVERT: R 38 LEU cc_start: 0.9762 (mm) cc_final: 0.9556 (tm) REVERT: R 39 TYR cc_start: 0.9002 (t80) cc_final: 0.8433 (t80) REVERT: R 136 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8870 (mtpp) REVERT: R 231 MET cc_start: 0.8927 (ttp) cc_final: 0.8663 (ttp) REVERT: R 385 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8370 (m-30) outliers start: 20 outliers final: 13 residues processed: 156 average time/residue: 1.1964 time to fit residues: 199.4741 Evaluate side-chains 148 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 10.0000 chunk 13 optimal weight: 0.0030 chunk 25 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 93 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 79 optimal weight: 0.0060 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 overall best weight: 0.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN N 39 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.109425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.072172 restraints weight = 18280.906| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.64 r_work: 0.2947 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9271 Z= 0.183 Angle : 0.709 11.000 12580 Z= 0.353 Chirality : 0.042 0.320 1412 Planarity : 0.005 0.069 1609 Dihedral : 5.330 48.268 1302 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.66 % Favored : 95.00 % Rotamer: Outliers : 1.62 % Allowed : 31.14 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.03 (0.25), residues: 1160 helix: 1.05 (0.26), residues: 461 sheet: 0.07 (0.36), residues: 204 loop : -1.06 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 115 HIS 0.006 0.001 HIS R 45 PHE 0.008 0.001 PHE R 391 TYR 0.017 0.001 TYR R 145 ARG 0.014 0.000 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4069.87 seconds wall clock time: 71 minutes 44.33 seconds (4304.33 seconds total)