Starting phenix.real_space_refine on Fri Jul 3 05:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ydz_72841/07_2026/9ydz_72841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ydz_72841/07_2026/9ydz_72841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ydz_72841/07_2026/9ydz_72841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ydz_72841/07_2026/9ydz_72841.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ydz_72841/07_2026/9ydz_72841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ydz_72841/07_2026/9ydz_72841.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.000 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 76 5.16 5 C 7864 2.51 5 N 2209 2.21 5 O 2066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12219 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2627 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2652 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2652 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2652 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 408 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 86 Chain: "F" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 408 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 86 Chain: "G" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 408 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 86 Chain: "H" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 408 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 86 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 3.08, per 1000 atoms: 0.25 Number of scatterers: 12219 At special positions: 0 Unit cell: (130.72, 130.72, 98.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 76 16.00 O 2066 8.00 N 2209 7.00 C 7864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 556.2 milliseconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3016 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 9 through 51 removed outlier: 3.908A pdb=" N ARG A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 removed outlier: 3.780A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.884A pdb=" N ALA A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 100 " --> pdb=" O TRP A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 100' Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.767A pdb=" N GLY A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 removed outlier: 3.609A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 161 through 170 removed outlier: 4.391A pdb=" N ARG A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.640A pdb=" N ALA A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.513A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 4.361A pdb=" N LEU A 207 " --> pdb=" O HIS A 203 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.906A pdb=" N VAL A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.631A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.600A pdb=" N LEU A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 289 removed outlier: 3.574A pdb=" N CYS A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N CYS A 277 " --> pdb=" O MET A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 332 removed outlier: 3.726A pdb=" N LYS A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 366 removed outlier: 4.161A pdb=" N ARG A 339 " --> pdb=" O HIS A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 51 removed outlier: 4.269A pdb=" N LYS B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 92 removed outlier: 3.790A pdb=" N THR B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA B 78 " --> pdb=" O CYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 146 through 155 removed outlier: 3.538A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.610A pdb=" N ARG B 159 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 161' Processing helix chain 'B' and resid 162 through 172 removed outlier: 4.132A pdb=" N GLY B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.000A pdb=" N LEU B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 removed outlier: 3.793A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.541A pdb=" N TRP B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 Processing helix chain 'B' and resid 236 through 244 removed outlier: 5.015A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 271 through 289 removed outlier: 3.737A pdb=" N CYS B 277 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 332 Processing helix chain 'B' and resid 337 through 366 removed outlier: 3.728A pdb=" N GLN B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 50 removed outlier: 3.786A pdb=" N GLY C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 54 removed outlier: 3.843A pdb=" N TRP C 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 54' Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.918A pdb=" N ILE C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS C 74 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.852A pdb=" N LEU C 100 " --> pdb=" O TRP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 116 Processing helix chain 'C' and resid 149 through 155 removed outlier: 3.528A pdb=" N LEU C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.604A pdb=" N ARG C 159 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 160' Processing helix chain 'C' and resid 161 through 170 removed outlier: 4.535A pdb=" N ARG C 165 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 191 through 203 removed outlier: 3.621A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 219 removed outlier: 3.974A pdb=" N TRP C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 236 through 244 removed outlier: 4.959A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.645A pdb=" N LEU C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 270 removed outlier: 3.800A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 289 removed outlier: 3.740A pdb=" N THR C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 332 removed outlier: 3.508A pdb=" N LYS C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 306 " --> pdb=" O MET C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 366 Processing helix chain 'D' and resid 10 through 33 removed outlier: 3.780A pdb=" N LEU D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 51 removed outlier: 4.156A pdb=" N ILE D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 73 removed outlier: 4.013A pdb=" N ILE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 92 Processing helix chain 'D' and resid 101 through 115 removed outlier: 3.589A pdb=" N ALA D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 155 removed outlier: 3.814A pdb=" N LEU D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'D' and resid 161 through 171 removed outlier: 4.462A pdb=" N ARG D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 217 through 227 removed outlier: 3.898A pdb=" N VAL D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 5.016A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.566A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 265 Processing helix chain 'D' and resid 268 through 289 removed outlier: 3.812A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS D 277 " --> pdb=" O MET D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 332 removed outlier: 3.699A pdb=" N LYS D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 366 Processing helix chain 'E' and resid 84 through 92 removed outlier: 3.972A pdb=" N PHE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 112 removed outlier: 3.662A pdb=" N LEU E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'F' and resid 84 through 92 removed outlier: 3.941A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 112 removed outlier: 3.815A pdb=" N LEU F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'G' and resid 84 through 92 removed outlier: 3.982A pdb=" N PHE G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 112 removed outlier: 3.605A pdb=" N LEU G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 142 through 147 Processing helix chain 'H' and resid 84 through 92 removed outlier: 4.071A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 112 removed outlier: 3.606A pdb=" N LEU H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 142 through 147 828 hydrogen bonds defined for protein. 2472 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: 1.61 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3993 1.34 - 1.46: 1633 1.46 - 1.57: 6701 1.57 - 1.69: 0 1.69 - 1.81: 124 Bond restraints: 12451 Sorted by residual: bond pdb=" C ILE C 246 " pdb=" O ILE C 246 " ideal model delta sigma weight residual 1.239 1.228 0.011 1.13e-02 7.83e+03 9.30e-01 bond pdb=" CG LEU C 361 " pdb=" CD2 LEU C 361 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.22e-01 bond pdb=" C ILE D 246 " pdb=" O ILE D 246 " ideal model delta sigma weight residual 1.239 1.228 0.011 1.13e-02 7.83e+03 8.79e-01 bond pdb=" C ILE A 246 " pdb=" O ILE A 246 " ideal model delta sigma weight residual 1.239 1.229 0.010 1.13e-02 7.83e+03 7.79e-01 bond pdb=" C VAL F 142 " pdb=" O VAL F 142 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.19e-02 7.06e+03 7.28e-01 ... (remaining 12446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 16692 1.85 - 3.69: 158 3.69 - 5.54: 31 5.54 - 7.38: 7 7.38 - 9.23: 1 Bond angle restraints: 16889 Sorted by residual: angle pdb=" N VAL G 142 " pdb=" CA VAL G 142 " pdb=" C VAL G 142 " ideal model delta sigma weight residual 113.53 108.19 5.34 9.80e-01 1.04e+00 2.97e+01 angle pdb=" N VAL E 142 " pdb=" CA VAL E 142 " pdb=" C VAL E 142 " ideal model delta sigma weight residual 113.53 108.98 4.55 9.80e-01 1.04e+00 2.15e+01 angle pdb=" N VAL H 142 " pdb=" CA VAL H 142 " pdb=" C VAL H 142 " ideal model delta sigma weight residual 113.53 109.05 4.48 9.80e-01 1.04e+00 2.09e+01 angle pdb=" N THR B 247 " pdb=" CA THR B 247 " pdb=" C THR B 247 " ideal model delta sigma weight residual 113.55 108.21 5.34 1.26e+00 6.30e-01 1.80e+01 angle pdb=" C LEU B 162 " pdb=" N VAL B 163 " pdb=" CA VAL B 163 " ideal model delta sigma weight residual 120.33 122.65 -2.32 8.00e-01 1.56e+00 8.39e+00 ... (remaining 16884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 6623 16.82 - 33.65: 515 33.65 - 50.47: 136 50.47 - 67.30: 24 67.30 - 84.12: 11 Dihedral angle restraints: 7309 sinusoidal: 2645 harmonic: 4664 Sorted by residual: dihedral pdb=" CA LEU F 116 " pdb=" C LEU F 116 " pdb=" N THR F 117 " pdb=" CA THR F 117 " ideal model delta harmonic sigma weight residual -180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LEU E 116 " pdb=" C LEU E 116 " pdb=" N THR E 117 " pdb=" CA THR E 117 " ideal model delta harmonic sigma weight residual 180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU G 116 " pdb=" C LEU G 116 " pdb=" N THR G 117 " pdb=" CA THR G 117 " ideal model delta harmonic sigma weight residual 180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 7306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1309 0.031 - 0.062: 511 0.062 - 0.092: 138 0.092 - 0.123: 23 0.123 - 0.154: 8 Chirality restraints: 1989 Sorted by residual: chirality pdb=" CB ILE D 251 " pdb=" CA ILE D 251 " pdb=" CG1 ILE D 251 " pdb=" CG2 ILE D 251 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CB ILE B 251 " pdb=" CA ILE B 251 " pdb=" CG1 ILE B 251 " pdb=" CG2 ILE B 251 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CB ILE A 251 " pdb=" CA ILE A 251 " pdb=" CG1 ILE A 251 " pdb=" CG2 ILE A 251 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1986 not shown) Planarity restraints: 2101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 334 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C SER C 334 " 0.031 2.00e-02 2.50e+03 pdb=" O SER C 334 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS C 335 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 117 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C THR F 117 " 0.024 2.00e-02 2.50e+03 pdb=" O THR F 117 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP F 118 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 117 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C THR E 117 " 0.022 2.00e-02 2.50e+03 pdb=" O THR E 117 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP E 118 " -0.007 2.00e-02 2.50e+03 ... (remaining 2098 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 4090 2.85 - 3.43: 13894 3.43 - 4.00: 20775 4.00 - 4.57: 29830 4.57 - 5.14: 41029 Nonbonded interactions: 109618 Sorted by model distance: nonbonded pdb=" OE1 GLU C 313 " pdb=" NH1 ARG C 317 " model vdw 2.283 3.120 nonbonded pdb=" OE1 GLU D 313 " pdb=" NH1 ARG D 317 " model vdw 2.284 3.120 nonbonded pdb=" O ALA C 336 " pdb=" ND1 HIS C 340 " model vdw 2.288 3.120 nonbonded pdb=" O LYS D 197 " pdb=" ND2 ASN D 201 " model vdw 2.314 3.120 nonbonded pdb=" OE1 GLU A 313 " pdb=" NH1 ARG A 317 " model vdw 2.324 3.120 ... (remaining 109613 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 366) selection = (chain 'B' and (resid 9 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 180 or (resid 181 through 182 and ( \ name N or name CA or name C or name O or name CB )) or (resid 183 through 185 an \ d (name N or name CA or name C or name O or name CB )) or resid 186 or (resid 18 \ 7 through 189 and (name N or name CA or name C or name O or name CB )) or resid \ 190 through 366)) selection = (chain 'C' and (resid 9 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 180 or (resid 181 through 182 and ( \ name N or name CA or name C or name O or name CB )) or (resid 183 through 185 an \ d (name N or name CA or name C or name O or name CB )) or resid 186 or (resid 18 \ 7 through 189 and (name N or name CA or name C or name O or name CB )) or resid \ 190 through 366)) selection = (chain 'D' and (resid 9 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 180 or (resid 181 through 182 and ( \ name N or name CA or name C or name O or name CB )) or (resid 183 through 185 an \ d (name N or name CA or name C or name O or name CB )) or resid 186 or (resid 18 \ 7 through 189 and (name N or name CA or name C or name O or name CB )) or resid \ 190 through 366)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 9.940 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.410 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.002 0.032 12451 Z= 0.104 Angle : 0.506 9.228 16889 Z= 0.291 Chirality : 0.035 0.154 1989 Planarity : 0.002 0.024 2101 Dihedral : 13.748 84.122 4293 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1604 helix: 0.96 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -1.77 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 331 TYR 0.006 0.001 TYR A 161 PHE 0.008 0.001 PHE A 59 TRP 0.014 0.001 TRP C 323 HIS 0.010 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.10 (12451) covalent geometry : angle 0.50620 / 0.29 (16889) hydrogen bonds : bond 0.13910 / 9.97 ( 828) hydrogen bonds : angle 4.81622 / 3.48 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.362 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: D 227 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7125 (mt-10) REVERT: D 255 ASP cc_start: 0.7379 (p0) cc_final: 0.6646 (p0) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1229 time to fit residues: 43.2461 Evaluate side-chains 197 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.0470 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS D 192 HIS D 201 ASN D 300 ASN ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.221403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.167024 restraints weight = 13832.896| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 6.75 r_work: 0.3303 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12451 Z= 0.154 Angle : 0.549 8.294 16889 Z= 0.287 Chirality : 0.038 0.120 1989 Planarity : 0.004 0.036 2101 Dihedral : 3.923 20.928 1746 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.98 % Allowed : 8.70 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1604 helix: 1.15 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -1.29 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 352 TYR 0.010 0.001 TYR D 307 PHE 0.015 0.001 PHE B 291 TRP 0.011 0.001 TRP B 242 HIS 0.012 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (12451) covalent geometry : angle 0.54911 / 0.29 (16889) hydrogen bonds : bond 0.04819 / 3.22 ( 828) hydrogen bonds : angle 3.81975 / 2.80 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7769 (mmt) cc_final: 0.7400 (mmt) REVERT: B 40 MET cc_start: 0.8158 (tmm) cc_final: 0.7954 (tmm) REVERT: C 71 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7582 (tt) REVERT: C 303 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7549 (mtp) REVERT: C 338 ARG cc_start: 0.7112 (ptt-90) cc_final: 0.6772 (mtm180) REVERT: G 139 GLU cc_start: 0.8671 (tp30) cc_final: 0.8410 (mm-30) REVERT: H 145 MET cc_start: 0.5892 (ptp) cc_final: 0.5430 (ptt) outliers start: 23 outliers final: 15 residues processed: 199 average time/residue: 0.0944 time to fit residues: 27.8121 Evaluate side-chains 198 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain H residue 84 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 358 HIS D 300 ASN D 358 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.214033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.185211 restraints weight = 14139.039| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.46 r_work: 0.3902 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12451 Z= 0.220 Angle : 0.617 9.631 16889 Z= 0.323 Chirality : 0.041 0.138 1989 Planarity : 0.004 0.048 2101 Dihedral : 4.292 21.325 1746 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.41 % Allowed : 13.18 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1604 helix: 0.99 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : -1.38 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 317 TYR 0.011 0.001 TYR B 253 PHE 0.018 0.002 PHE D 291 TRP 0.017 0.002 TRP B 242 HIS 0.013 0.002 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 (12451) covalent geometry : angle 0.61679 / 0.32 (16889) hydrogen bonds : bond 0.05565 / 3.67 ( 828) hydrogen bonds : angle 3.95228 / 2.89 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7827 (tt) REVERT: F 145 MET cc_start: 0.4415 (ptt) cc_final: 0.4170 (ptp) REVERT: G 145 MET cc_start: 0.4427 (ptt) cc_final: 0.4034 (ptp) REVERT: H 83 GLU cc_start: 0.5513 (tp30) cc_final: 0.4492 (mp0) outliers start: 28 outliers final: 20 residues processed: 200 average time/residue: 0.1026 time to fit residues: 30.0989 Evaluate side-chains 193 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain H residue 84 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 146 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 136 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 140 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN ** F 107 HIS ** 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 = 0.4448 r_free = 0.4448 target = 0.220170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171862 restraints weight = 14113.422| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 5.26 r_work: 0.3509 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12451 Z= 0.128 Angle : 0.502 7.220 16889 Z= 0.267 Chirality : 0.036 0.115 1989 Planarity : 0.003 0.028 2101 Dihedral : 4.009 20.340 1746 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.19 % Allowed : 15.68 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.22), residues: 1604 helix: 1.22 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : -1.41 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.014 0.001 TYR G 138 PHE 0.013 0.001 PHE D 291 TRP 0.021 0.001 TRP A 323 HIS 0.011 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (12451) covalent geometry : angle 0.50159 / 0.27 (16889) hydrogen bonds : bond 0.04350 / 2.86 ( 828) hydrogen bonds : angle 3.69052 / 2.71 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7693 (tt) REVERT: C 255 ASP cc_start: 0.7639 (p0) cc_final: 0.7417 (p0) REVERT: F 145 MET cc_start: 0.6027 (ptt) cc_final: 0.5556 (ptp) REVERT: G 145 MET cc_start: 0.6043 (ptt) cc_final: 0.5479 (ptp) REVERT: H 83 GLU cc_start: 0.5847 (tp30) cc_final: 0.4298 (mp0) REVERT: H 145 MET cc_start: 0.6212 (ptt) cc_final: 0.5952 (ptp) outliers start: 37 outliers final: 25 residues processed: 206 average time/residue: 0.0986 time to fit residues: 30.1221 Evaluate side-chains 203 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain H residue 84 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 125 optimal weight: 0.0070 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 300 ASN D 358 HIS ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.213546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189205 restraints weight = 14107.300| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.15 r_work: 0.3931 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12451 Z= 0.220 Angle : 0.604 8.679 16889 Z= 0.318 Chirality : 0.040 0.138 1989 Planarity : 0.004 0.041 2101 Dihedral : 4.305 21.701 1746 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.70 % Allowed : 17.05 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1604 helix: 1.06 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : -1.45 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 317 TYR 0.010 0.001 TYR B 253 PHE 0.018 0.001 PHE D 291 TRP 0.018 0.002 TRP A 323 HIS 0.009 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.22 (12451) covalent geometry : angle 0.60429 / 0.32 (16889) hydrogen bonds : bond 0.05421 / 3.57 ( 828) hydrogen bonds : angle 3.90430 / 2.85 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 VAL cc_start: 0.8745 (p) cc_final: 0.8536 (p) REVERT: C 71 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7843 (tt) outliers start: 43 outliers final: 29 residues processed: 212 average time/residue: 0.1026 time to fit residues: 32.2475 Evaluate side-chains 205 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain H residue 84 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 137 optimal weight: 0.0870 chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 109 optimal weight: 0.0570 chunk 156 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 120 optimal weight: 0.1980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.221061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.176565 restraints weight = 14045.368| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 4.60 r_work: 0.3607 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.003 0.029 12451 Z= 0.119 Angle : 0.505 6.380 16889 Z= 0.268 Chirality : 0.035 0.149 1989 Planarity : 0.003 0.028 2101 Dihedral : 3.996 19.798 1746 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.36 % Allowed : 18.95 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1604 helix: 1.25 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 317 TYR 0.007 0.001 TYR F 138 PHE 0.018 0.001 PHE D 301 TRP 0.018 0.001 TRP A 323 HIS 0.007 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12451) covalent geometry : angle 0.50531 / 0.27 (16889) hydrogen bonds : bond 0.04133 / 2.71 ( 828) hydrogen bonds : angle 3.64533 / 2.67 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 255 ASP cc_start: 0.7820 (p0) cc_final: 0.7607 (p0) REVERT: C 71 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7704 (tt) REVERT: D 255 ASP cc_start: 0.7793 (p0) cc_final: 0.7550 (p0) REVERT: F 139 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6222 (mp0) REVERT: H 83 GLU cc_start: 0.5701 (tp30) cc_final: 0.4066 (mp0) outliers start: 39 outliers final: 28 residues processed: 203 average time/residue: 0.0993 time to fit residues: 30.2255 Evaluate side-chains 199 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 335 HIS Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain H residue 84 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 18 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS A 364 GLN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.221200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169865 restraints weight = 14095.335| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 5.94 r_work: 0.3261 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12451 Z= 0.119 Angle : 0.512 7.005 16889 Z= 0.273 Chirality : 0.035 0.139 1989 Planarity : 0.003 0.028 2101 Dihedral : 3.903 19.387 1746 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.93 % Allowed : 19.38 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1604 helix: 1.20 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -1.41 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 317 TYR 0.011 0.001 TYR F 138 PHE 0.012 0.001 PHE D 291 TRP 0.018 0.001 TRP A 323 HIS 0.010 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (12451) covalent geometry : angle 0.51198 / 0.27 (16889) hydrogen bonds : bond 0.04070 / 2.68 ( 828) hydrogen bonds : angle 3.60687 / 2.64 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 302 MET cc_start: 0.8968 (mtm) cc_final: 0.8611 (mtm) REVERT: B 303 MET cc_start: 0.7665 (mmp) cc_final: 0.7159 (mtp) REVERT: B 320 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8681 (tm-30) REVERT: C 71 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7590 (tt) REVERT: C 302 MET cc_start: 0.9260 (mtm) cc_final: 0.8993 (mtp) REVERT: C 306 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7875 (mp10) REVERT: D 301 PHE cc_start: 0.8233 (t80) cc_final: 0.8009 (t80) REVERT: F 139 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6682 (mp0) REVERT: F 145 MET cc_start: 0.6532 (ptt) cc_final: 0.6084 (ptp) REVERT: H 83 GLU cc_start: 0.5861 (tp30) cc_final: 0.4075 (mp0) REVERT: H 145 MET cc_start: 0.5384 (ptp) cc_final: 0.5165 (ptp) outliers start: 34 outliers final: 24 residues processed: 201 average time/residue: 0.0944 time to fit residues: 28.5956 Evaluate side-chains 202 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 335 HIS Chi-restraints excluded: chain H residue 84 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 105 optimal weight: 0.6980 chunk 45 optimal weight: 0.0670 chunk 64 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS B 306 GLN B 340 HIS ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.218716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.192724 restraints weight = 14043.046| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.41 r_work: 0.3977 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12451 Z= 0.124 Angle : 0.533 7.914 16889 Z= 0.285 Chirality : 0.036 0.151 1989 Planarity : 0.003 0.028 2101 Dihedral : 3.902 19.121 1746 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.19 % Allowed : 19.04 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1604 helix: 1.29 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -1.35 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 317 TYR 0.009 0.001 TYR F 138 PHE 0.013 0.001 PHE C 301 TRP 0.019 0.001 TRP A 323 HIS 0.008 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (12451) covalent geometry : angle 0.53342 / 0.29 (16889) hydrogen bonds : bond 0.04140 / 2.73 ( 828) hydrogen bonds : angle 3.62685 / 2.64 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7755 (tt) REVERT: F 83 GLU cc_start: 0.5537 (tp30) cc_final: 0.4548 (mp0) REVERT: H 83 GLU cc_start: 0.5421 (tp30) cc_final: 0.4295 (mp0) REVERT: H 145 MET cc_start: 0.3549 (ptp) cc_final: 0.3178 (ptt) outliers start: 37 outliers final: 33 residues processed: 199 average time/residue: 0.0927 time to fit residues: 27.9260 Evaluate side-chains 206 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 335 HIS Chi-restraints excluded: chain H residue 84 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 69 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 358 HIS ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 HIS ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.217710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.189222 restraints weight = 13927.445| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.46 r_work: 0.3949 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12451 Z= 0.141 Angle : 0.546 8.686 16889 Z= 0.291 Chirality : 0.036 0.131 1989 Planarity : 0.003 0.028 2101 Dihedral : 3.948 19.312 1746 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.53 % Allowed : 19.29 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1604 helix: 1.29 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -1.32 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 317 TYR 0.006 0.001 TYR C 179 PHE 0.014 0.001 PHE D 291 TRP 0.019 0.001 TRP A 323 HIS 0.009 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (12451) covalent geometry : angle 0.54575 / 0.29 (16889) hydrogen bonds : bond 0.04342 / 2.86 ( 828) hydrogen bonds : angle 3.65986 / 2.66 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7738 (tt) REVERT: F 83 GLU cc_start: 0.5557 (tp30) cc_final: 0.4500 (mp0) REVERT: F 145 MET cc_start: 0.3890 (ptp) cc_final: 0.3578 (ptt) REVERT: H 83 GLU cc_start: 0.5575 (tp30) cc_final: 0.4400 (mp0) REVERT: H 145 MET cc_start: 0.3811 (ptp) cc_final: 0.3463 (ptt) outliers start: 41 outliers final: 37 residues processed: 201 average time/residue: 0.1019 time to fit residues: 30.6655 Evaluate side-chains 211 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 335 HIS Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain H residue 84 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.0370 chunk 159 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 79 optimal weight: 0.0020 overall best weight: 0.5866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS D 203 HIS ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.220951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.162110 restraints weight = 14004.867| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 8.22 r_work: 0.3223 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12451 Z= 0.134 Angle : 0.545 7.574 16889 Z= 0.293 Chirality : 0.036 0.120 1989 Planarity : 0.003 0.028 2101 Dihedral : 3.911 20.084 1746 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.36 % Allowed : 19.21 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1604 helix: 1.29 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -1.33 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 317 TYR 0.011 0.001 TYR C 307 PHE 0.019 0.001 PHE C 301 TRP 0.019 0.001 TRP A 323 HIS 0.009 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (12451) covalent geometry : angle 0.54540 / 0.29 (16889) hydrogen bonds : bond 0.04214 / 2.78 ( 828) hydrogen bonds : angle 3.65472 / 2.66 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 303 MET cc_start: 0.7547 (mmp) cc_final: 0.7057 (mtp) REVERT: C 71 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7542 (tt) REVERT: C 302 MET cc_start: 0.9133 (mtm) cc_final: 0.8830 (mtm) REVERT: C 306 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8077 (mp10) REVERT: C 307 TYR cc_start: 0.9059 (m-10) cc_final: 0.8757 (m-10) REVERT: F 83 GLU cc_start: 0.5943 (tp30) cc_final: 0.4161 (mp0) REVERT: F 145 MET cc_start: 0.5822 (ptp) cc_final: 0.5188 (ptt) REVERT: H 83 GLU cc_start: 0.5966 (tp30) cc_final: 0.4166 (mp0) REVERT: H 145 MET cc_start: 0.5836 (ptp) cc_final: 0.5189 (ptt) outliers start: 39 outliers final: 36 residues processed: 203 average time/residue: 0.0932 time to fit residues: 28.5821 Evaluate side-chains 213 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 335 HIS Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain H residue 84 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 0.0470 chunk 68 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 154 optimal weight: 0.0370 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.223024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197651 restraints weight = 13982.180| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.23 r_work: 0.3902 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12451 Z= 0.115 Angle : 0.532 8.176 16889 Z= 0.288 Chirality : 0.035 0.130 1989 Planarity : 0.003 0.029 2101 Dihedral : 3.790 19.633 1746 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.76 % Allowed : 19.98 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1604 helix: 1.23 (0.15), residues: 1244 sheet: None (None), residues: 0 loop : -1.36 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 317 TYR 0.007 0.001 TYR C 307 PHE 0.012 0.001 PHE D 291 TRP 0.031 0.001 TRP A 323 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (12451) covalent geometry : angle 0.53222 / 0.29 (16889) hydrogen bonds : bond 0.03901 / 2.57 ( 828) hydrogen bonds : angle 3.58529 / 2.61 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3028.64 seconds wall clock time: 52 minutes 40.68 seconds (3160.68 seconds total)