Starting phenix.real_space_refine on Mon Aug 25 02:13:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smr_40601/08_2025/8smr_40601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smr_40601/08_2025/8smr_40601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8smr_40601/08_2025/8smr_40601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smr_40601/08_2025/8smr_40601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8smr_40601/08_2025/8smr_40601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smr_40601/08_2025/8smr_40601.map" } resolution = 2.7 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= 0.002 sd= 0.182 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 19 7.16 5 Cu 1 5.60 5 S 141 5.16 5 C 15890 2.51 5 N 3934 2.21 5 O 4167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24154 Number of models: 1 Model: "" Number of chains: 24 Chain: "C" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1420 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 20, 'TRANS': 169} Chain: "I" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3267 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "J" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1842 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 13, 'TRANS': 218} Chain: "K" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1306 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "L" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 115 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "Z" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1449 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 20, 'TRANS': 173} Chain: "D" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3267 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "M" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1631 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "N" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1306 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "O" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 115 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 452} Chain: "F" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1499 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 188} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "G" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2345 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 16, 'TRANS': 295} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'HEM': 2, 'I7Y': 1, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 11 Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'FES': 1, 'I7Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'HEM': 2, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 89 Unusual residues: {' CA': 2, ' CU': 1, 'HEM': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 878 SG CYS C 124 85.827 89.782 77.166 1.00 85.05 S ATOM 913 SG CYS C 129 82.197 90.933 76.398 1.00 88.42 S ATOM 1090 SG CYS C 152 83.421 92.466 78.335 1.00 90.53 S ATOM 8848 SG CYS Z 124 43.111 59.333 39.809 1.00 50.08 S ATOM 9060 SG CYS Z 152 46.380 59.925 38.108 1.00 53.09 S Time building chain proxies: 4.94, per 1000 atoms: 0.20 Number of scatterers: 24154 At special positions: 0 Unit cell: (114.33, 140.08, 159.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 1 28.99 Fe 19 26.01 Ca 2 19.99 S 141 16.00 O 4167 8.00 N 3934 7.00 C 15890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 165 " - pdb=" SG CYS J 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 843.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 155 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 126 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 152 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 124 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 129 " pdb=" FES Z 201 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 155 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 126 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 152 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 124 " Number of angles added : 9 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5452 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 19 sheets defined 61.7% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'C' and resid 7 through 36 Proline residue: C 32 - end of helix Processing helix chain 'C' and resid 40 through 47 Processing helix chain 'C' and resid 78 through 85 removed outlier: 3.528A pdb=" N LEU C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 4.364A pdb=" N GLU C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 92 " --> pdb=" O GLU C 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 12 removed outlier: 3.587A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 Processing helix chain 'I' and resid 32 through 35 Processing helix chain 'I' and resid 36 through 57 Processing helix chain 'I' and resid 65 through 76 Processing helix chain 'I' and resid 79 through 108 Processing helix chain 'I' and resid 115 through 139 removed outlier: 3.520A pdb=" N LEU I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU I 139 " --> pdb=" O MET I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 156 removed outlier: 3.992A pdb=" N PHE I 156 " --> pdb=" O ILE I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'I' and resid 162 through 172 Processing helix chain 'I' and resid 177 through 190 Processing helix chain 'I' and resid 190 through 211 Processing helix chain 'I' and resid 219 through 223 Processing helix chain 'I' and resid 236 through 262 removed outlier: 6.667A pdb=" N THR I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 276 Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 293 through 303 Processing helix chain 'I' and resid 305 through 327 removed outlier: 3.663A pdb=" N ILE I 317 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU I 320 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 322 " --> pdb=" O ALA I 318 " (cutoff:3.500A) Proline residue: I 324 - end of helix Processing helix chain 'I' and resid 333 through 337 Processing helix chain 'I' and resid 338 through 360 Processing helix chain 'I' and resid 364 through 384 removed outlier: 3.918A pdb=" N PHE I 382 " --> pdb=" O TYR I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 392 removed outlier: 4.255A pdb=" N ARG I 390 " --> pdb=" O PRO I 386 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I 392 " --> pdb=" O TYR I 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 51 Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 72 through 80 Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 119 through 128 removed outlier: 3.546A pdb=" N ARG J 128 " --> pdb=" O TYR J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 159 Processing helix chain 'J' and resid 204 through 224 Processing helix chain 'J' and resid 226 through 254 Processing helix chain 'K' and resid 23 through 31 removed outlier: 3.956A pdb=" N ALA K 29 " --> pdb=" O ALA K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 56 through 69 Processing helix chain 'K' and resid 74 through 78 Processing helix chain 'K' and resid 85 through 98 Processing helix chain 'K' and resid 107 through 121 removed outlier: 4.569A pdb=" N ALA K 112 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN K 113 " --> pdb=" O ASN K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 Processing helix chain 'K' and resid 176 through 184 removed outlier: 3.878A pdb=" N LYS K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 199 removed outlier: 3.547A pdb=" N GLY K 199 " --> pdb=" O SER K 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'Z' and resid 9 through 36 Proline residue: Z 32 - end of helix Processing helix chain 'Z' and resid 42 through 46 removed outlier: 3.532A pdb=" N ALA Z 45 " --> pdb=" O LYS Z 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA Z 46 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 46' Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 86 through 92 removed outlier: 4.822A pdb=" N GLY Z 90 " --> pdb=" O SER Z 87 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Z 92 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.598A pdb=" N ARG D 11 " --> pdb=" O TRP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 32 through 35 Processing helix chain 'D' and resid 36 through 57 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 79 through 109 Processing helix chain 'D' and resid 115 through 139 removed outlier: 3.576A pdb=" N LEU D 139 " --> pdb=" O MET D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 156 removed outlier: 4.063A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'D' and resid 190 through 211 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 236 through 262 removed outlier: 6.719A pdb=" N THR D 241 " --> pdb=" O HIS D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 303 removed outlier: 3.596A pdb=" N VAL D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 322 removed outlier: 4.103A pdb=" N LEU D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 338 through 359 Processing helix chain 'D' and resid 364 through 384 removed outlier: 3.879A pdb=" N PHE D 382 " --> pdb=" O TYR D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 392 removed outlier: 4.342A pdb=" N ARG D 390 " --> pdb=" O PRO D 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 51 Processing helix chain 'M' and resid 62 through 70 Processing helix chain 'M' and resid 72 through 80 Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 113 through 118 Processing helix chain 'M' and resid 119 through 128 removed outlier: 3.541A pdb=" N ARG M 128 " --> pdb=" O TYR M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 159 Processing helix chain 'M' and resid 204 through 224 Processing helix chain 'M' and resid 226 through 256 removed outlier: 3.610A pdb=" N TYR M 236 " --> pdb=" O ARG M 232 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE M 247 " --> pdb=" O PHE M 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 31 removed outlier: 3.866A pdb=" N ALA N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 Processing helix chain 'N' and resid 56 through 69 Processing helix chain 'N' and resid 74 through 78 Processing helix chain 'N' and resid 85 through 98 Processing helix chain 'N' and resid 107 through 121 removed outlier: 4.662A pdb=" N ALA N 112 " --> pdb=" O PRO N 108 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLN N 113 " --> pdb=" O ASN N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 166 Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'N' and resid 186 through 199 Processing helix chain 'O' and resid 25 through 29 Processing helix chain 'E' and resid 11 through 42 removed outlier: 4.040A pdb=" N VAL E 15 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 49 through 52 Processing helix chain 'E' and resid 53 through 68 Proline residue: E 59 - end of helix removed outlier: 3.778A pdb=" N ILE E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 87 removed outlier: 4.165A pdb=" N GLN E 83 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 114 Processing helix chain 'E' and resid 133 through 152 Processing helix chain 'E' and resid 159 through 180 removed outlier: 5.108A pdb=" N HIS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 211 removed outlier: 4.083A pdb=" N ASN E 209 " --> pdb=" O TRP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 232 Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 237 through 253 removed outlier: 4.409A pdb=" N ILE E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 261 removed outlier: 3.617A pdb=" N HIS E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS E 261 " --> pdb=" O HIS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 294 removed outlier: 4.386A pdb=" N ALA E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Proline residue: E 283 - end of helix Processing helix chain 'E' and resid 298 through 304 Processing helix chain 'E' and resid 305 through 329 Proline residue: E 326 - end of helix Processing helix chain 'E' and resid 330 through 337 removed outlier: 3.919A pdb=" N LEU E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 352 removed outlier: 4.222A pdb=" N ILE E 344 " --> pdb=" O THR E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 371 Proline residue: E 368 - end of helix Processing helix chain 'E' and resid 378 through 413 removed outlier: 3.861A pdb=" N GLY E 392 " --> pdb=" O LEU E 388 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU E 395 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 396 " --> pdb=" O GLY E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 461 Proline residue: E 433 - end of helix Processing helix chain 'E' and resid 464 through 473 removed outlier: 3.871A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 4.292A pdb=" N LEU F 7 " --> pdb=" O ASN F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 30 removed outlier: 4.066A pdb=" N GLY F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR F 28 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F 29 " --> pdb=" O GLY F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 64 through 68 removed outlier: 3.686A pdb=" N GLY F 67 " --> pdb=" O GLY F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.797A pdb=" N VAL F 93 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 127 through 132 removed outlier: 4.148A pdb=" N VAL F 131 " --> pdb=" O ASN F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 163 Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.555A pdb=" N ARG F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'G' and resid 2 through 28 Processing helix chain 'G' and resid 55 through 76 Processing helix chain 'G' and resid 103 through 127 Proline residue: G 121 - end of helix Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 137 through 152 Processing helix chain 'G' and resid 152 through 157 Processing helix chain 'G' and resid 179 through 190 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 230 through 241 removed outlier: 3.571A pdb=" N THR G 240 " --> pdb=" O GLN G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 283 Processing helix chain 'G' and resid 291 through 312 removed outlier: 3.847A pdb=" N LEU G 295 " --> pdb=" O GLN G 291 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASN G 297 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N ASP G 298 " --> pdb=" O HIS G 294 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 50 through 53 removed outlier: 6.810A pdb=" N THR C 189 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE C 182 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 67 Processing sheet with id=AA3, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AA4, first strand: chain 'I' and resid 26 through 28 Processing sheet with id=AA5, first strand: chain 'J' and resid 57 through 61 removed outlier: 3.780A pdb=" N MET J 91 " --> pdb=" O ALA J 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 130 through 132 Processing sheet with id=AA7, first strand: chain 'J' and resid 161 through 169 removed outlier: 6.185A pdb=" N VAL J 162 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU J 194 " --> pdb=" O VAL J 162 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY J 164 " --> pdb=" O ASP J 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'K' and resid 200 through 201 Processing sheet with id=AB1, first strand: chain 'Z' and resid 50 through 53 removed outlier: 6.695A pdb=" N THR Z 189 " --> pdb=" O PHE Z 182 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N PHE Z 182 " --> pdb=" O THR Z 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 61 through 67 removed outlier: 3.856A pdb=" N GLN Z 61 " --> pdb=" O HIS Z 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 132 through 134 Processing sheet with id=AB4, first strand: chain 'D' and resid 26 through 28 Processing sheet with id=AB5, first strand: chain 'M' and resid 57 through 61 removed outlier: 3.889A pdb=" N MET M 91 " --> pdb=" O ALA M 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 130 through 132 Processing sheet with id=AB7, first strand: chain 'M' and resid 161 through 162 Processing sheet with id=AB8, first strand: chain 'N' and resid 200 through 201 Processing sheet with id=AB9, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.828A pdb=" N LYS E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 191 through 192 1302 hydrogen bonds defined for protein. 3741 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: 3.89 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.36: 7519 1.36 - 1.57: 17094 1.57 - 1.78: 29 1.78 - 1.99: 232 1.99 - 2.21: 68 Bond restraints: 24942 Sorted by residual: bond pdb=" C07 I7Y Z 202 " pdb=" C08 I7Y Z 202 " ideal model delta sigma weight residual 1.542 1.253 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C07 I7Y I 504 " pdb=" C08 I7Y I 504 " ideal model delta sigma weight residual 1.542 1.253 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C07 I7Y I 504 " pdb=" C15 I7Y I 504 " ideal model delta sigma weight residual 1.526 1.775 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C07 I7Y Z 202 " pdb=" C15 I7Y Z 202 " ideal model delta sigma weight residual 1.526 1.775 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C02 I7Y I 504 " pdb=" C10 I7Y I 504 " ideal model delta sigma weight residual 1.526 1.295 0.231 2.00e-02 2.50e+03 1.33e+02 ... (remaining 24937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 34104 6.76 - 13.53: 40 13.53 - 20.29: 3 20.29 - 27.05: 0 27.05 - 33.82: 4 Bond angle restraints: 34151 Sorted by residual: angle pdb=" C74 I7Y I 504 " pdb=" C73 I7Y I 504 " pdb=" C76 I7Y I 504 " ideal model delta sigma weight residual 114.35 148.17 -33.82 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C74 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C76 I7Y Z 202 " ideal model delta sigma weight residual 114.35 148.16 -33.81 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C74 I7Y I 504 " pdb=" C73 I7Y I 504 " pdb=" O80 I7Y I 504 " ideal model delta sigma weight residual 107.63 79.89 27.74 3.00e+00 1.11e-01 8.55e+01 angle pdb=" C74 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" O80 I7Y Z 202 " ideal model delta sigma weight residual 107.63 79.90 27.73 3.00e+00 1.11e-01 8.54e+01 angle pdb=" CB GLN Z 169 " pdb=" CG GLN Z 169 " pdb=" CD GLN Z 169 " ideal model delta sigma weight residual 112.60 98.34 14.26 1.70e+00 3.46e-01 7.04e+01 ... (remaining 34146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 13154 24.23 - 48.47: 925 48.47 - 72.70: 168 72.70 - 96.94: 67 96.94 - 121.17: 15 Dihedral angle restraints: 14329 sinusoidal: 5768 harmonic: 8561 Sorted by residual: dihedral pdb=" C2B HEC J 500 " pdb=" C3B HEC J 500 " pdb=" CAB HEC J 500 " pdb=" CBB HEC J 500 " ideal model delta sinusoidal sigma weight residual 60.00 132.70 -72.70 2 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" C2C HEC N 501 " pdb=" C3C HEC N 501 " pdb=" CAC HEC N 501 " pdb=" CBC HEC N 501 " ideal model delta sinusoidal sigma weight residual 60.00 116.70 -56.70 2 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" C6 U10 D 503 " pdb=" C7 U10 D 503 " pdb=" C8 U10 D 503 " pdb=" C9 U10 D 503 " ideal model delta sinusoidal sigma weight residual 101.51 -147.21 -111.27 1 2.00e+01 2.50e-03 3.27e+01 ... (remaining 14326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 3583 0.282 - 0.565: 5 0.565 - 0.847: 2 0.847 - 1.130: 0 1.130 - 1.412: 2 Chirality restraints: 3592 Sorted by residual: chirality pdb=" C74 I7Y I 504 " pdb=" C03 I7Y I 504 " pdb=" C73 I7Y I 504 " pdb=" C75 I7Y I 504 " both_signs ideal model delta sigma weight residual False -2.55 -1.14 -1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" C74 I7Y Z 202 " pdb=" C03 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C75 I7Y Z 202 " both_signs ideal model delta sigma weight residual False -2.55 -1.14 -1.41 2.00e-01 2.50e+01 4.98e+01 chirality pdb=" C02 I7Y I 504 " pdb=" C03 I7Y I 504 " pdb=" C06 I7Y I 504 " pdb=" C10 I7Y I 504 " both_signs ideal model delta sigma weight residual False 2.93 2.25 0.68 2.00e-01 2.50e+01 1.14e+01 ... (remaining 3589 not shown) Planarity restraints: 4244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC N 501 " -0.025 2.00e-02 2.50e+03 6.32e-02 8.99e+01 pdb=" C2C HEC N 501 " 0.173 2.00e-02 2.50e+03 pdb=" C3C HEC N 501 " -0.016 2.00e-02 2.50e+03 pdb=" C4C HEC N 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC N 501 " -0.040 2.00e-02 2.50e+03 pdb=" CHC HEC N 501 " -0.031 2.00e-02 2.50e+03 pdb=" CHD HEC N 501 " 0.006 2.00e-02 2.50e+03 pdb=" CMC HEC N 501 " -0.048 2.00e-02 2.50e+03 pdb=" NC HEC N 501 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 501 " -0.018 2.00e-02 2.50e+03 5.68e-02 7.26e+01 pdb=" C2C HEC K 501 " 0.155 2.00e-02 2.50e+03 pdb=" C3C HEC K 501 " -0.037 2.00e-02 2.50e+03 pdb=" C4C HEC K 501 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC K 501 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEC K 501 " -0.027 2.00e-02 2.50e+03 pdb=" CHD HEC K 501 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC K 501 " -0.046 2.00e-02 2.50e+03 pdb=" NC HEC K 501 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC G 401 " -0.010 2.00e-02 2.50e+03 5.11e-02 5.87e+01 pdb=" C2C HEC G 401 " 0.137 2.00e-02 2.50e+03 pdb=" C3C HEC G 401 " -0.045 2.00e-02 2.50e+03 pdb=" C4C HEC G 401 " -0.006 2.00e-02 2.50e+03 pdb=" CAC HEC G 401 " -0.011 2.00e-02 2.50e+03 pdb=" CHC HEC G 401 " -0.025 2.00e-02 2.50e+03 pdb=" CHD HEC G 401 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC G 401 " -0.042 2.00e-02 2.50e+03 pdb=" NC HEC G 401 " -0.001 2.00e-02 2.50e+03 ... (remaining 4241 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 253 2.56 - 3.14: 20082 3.14 - 3.73: 42450 3.73 - 4.31: 59958 4.31 - 4.90: 97746 Nonbonded interactions: 220489 Sorted by model distance: nonbonded pdb=" OG SER F 135 " pdb=" O1D HEC F 301 " model vdw 1.975 3.040 nonbonded pdb=" OG SER N 85 " pdb=" OD1 ASP N 88 " model vdw 2.024 3.040 nonbonded pdb=" OG1 THR C 181 " pdb=" OE1 GLN C 194 " model vdw 2.054 3.040 nonbonded pdb=" O LEU N 75 " pdb=" OG1 THR N 78 " model vdw 2.096 3.040 nonbonded pdb=" OH TYR E 238 " pdb=" OE2 GLU F 8 " model vdw 2.097 3.040 ... (remaining 220484 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 'C' and resid 6 through 195) selection = (chain 'Z' and resid 6 through 195) } ncs_group { reference = chain 'D' selection = (chain 'I' and resid 1 through 503) } ncs_group { reference = (chain 'J' and (resid 26 through 163 or resid 193 through 500)) selection = (chain 'M' and resid 26 through 500) } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' } 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 22.970 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 : 0.009 0.377 24985 Z= 0.421 Angle : 0.902 35.633 34162 Z= 0.392 Chirality : 0.058 1.412 3592 Planarity : 0.005 0.063 4244 Dihedral : 18.183 121.174 8874 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 0.92 % Allowed : 19.42 % Favored : 79.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.77 (0.15), residues: 2972 helix: 1.10 (0.13), residues: 1628 sheet: -2.47 (0.63), residues: 46 loop : -0.01 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 253 TYR 0.014 0.001 TYR I 388 PHE 0.024 0.001 PHE I 255 TRP 0.015 0.001 TRP I 54 HIS 0.013 0.001 HIS Z 158 Details of bonding type rmsd covalent geometry : bond 0.00752 (24942) covalent geometry : angle 0.84181 (34151) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.27200 ( 2) hydrogen bonds : bond 0.13827 ( 1302) hydrogen bonds : angle 6.54112 ( 3741) metal coordination : bond 0.01173 ( 9) metal coordination : angle 20.06080 ( 9) Misc. bond : bond 0.15247 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 456 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 52 MET cc_start: 0.8975 (mtp) cc_final: 0.8678 (mtm) REVERT: K 23 ASP cc_start: 0.7961 (t0) cc_final: 0.7717 (t70) REVERT: Z 76 HIS cc_start: 0.8477 (t-90) cc_final: 0.8212 (t-90) REVERT: D 3 LYS cc_start: 0.7442 (mptt) cc_final: 0.6407 (mppt) REVERT: E 229 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8578 (mmmt) REVERT: E 261 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7421 (t-90) REVERT: E 410 MET cc_start: 0.8123 (mmm) cc_final: 0.7703 (mtm) REVERT: F 24 ILE cc_start: 0.7745 (mm) cc_final: 0.7469 (mp) REVERT: F 197 THR cc_start: 0.8972 (m) cc_final: 0.8746 (m) REVERT: G 45 ASP cc_start: 0.7812 (t70) cc_final: 0.7326 (t70) REVERT: G 195 MET cc_start: 0.8324 (tpt) cc_final: 0.7882 (tpt) outliers start: 22 outliers final: 15 residues processed: 469 average time/residue: 0.5769 time to fit residues: 311.5791 Evaluate side-chains 426 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 410 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 361 GLN Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 473 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 192 HIS Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN Z 158 HIS D 361 GLN N 201 HIS E 203 GLN ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN E 432 HIS F 127 ASN G 31 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS G 294 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102962 restraints weight = 27391.307| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.07 r_work: 0.2629 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.422 24985 Z= 0.183 Angle : 0.795 35.761 34162 Z= 0.331 Chirality : 0.045 0.235 3592 Planarity : 0.005 0.051 4244 Dihedral : 12.295 128.886 3696 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.85 % Allowed : 18.04 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 0.84 (0.15), residues: 2972 helix: 1.10 (0.13), residues: 1660 sheet: -2.31 (0.68), residues: 42 loop : 0.08 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 10 TYR 0.022 0.002 TYR C 105 PHE 0.027 0.002 PHE I 255 TRP 0.017 0.001 TRP D 147 HIS 0.008 0.001 HIS E 300 Details of bonding type rmsd covalent geometry : bond 0.00420 (24942) covalent geometry : angle 0.73309 (34151) SS BOND : bond 0.01025 ( 1) SS BOND : angle 2.21675 ( 2) hydrogen bonds : bond 0.05081 ( 1302) hydrogen bonds : angle 5.37778 ( 3741) metal coordination : bond 0.02355 ( 9) metal coordination : angle 18.89010 ( 9) Misc. bond : bond 0.17949 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 448 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8518 (tp-100) REVERT: J 34 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8644 (mt) REVERT: J 52 MET cc_start: 0.9056 (mtp) cc_final: 0.8792 (mtm) REVERT: K 28 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: L 34 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7732 (mmtm) REVERT: Z 75 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8761 (m) REVERT: Z 76 HIS cc_start: 0.8529 (t-90) cc_final: 0.8213 (t-90) REVERT: Z 147 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7995 (mtpp) REVERT: Z 164 ARG cc_start: 0.8604 (mtm180) cc_final: 0.8261 (mtm180) REVERT: D 3 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6573 (mppt) REVERT: D 308 MET cc_start: 0.8873 (tpt) cc_final: 0.8630 (tpp) REVERT: N 95 TYR cc_start: 0.9138 (t80) cc_final: 0.8850 (t80) REVERT: E 229 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8480 (mmmt) REVERT: E 239 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7553 (mmm-85) REVERT: E 410 MET cc_start: 0.8501 (mmm) cc_final: 0.8295 (mtm) REVERT: E 469 LEU cc_start: 0.8212 (mt) cc_final: 0.7986 (pp) REVERT: F 24 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7485 (mp) REVERT: F 127 ASN cc_start: 0.8778 (t0) cc_final: 0.8501 (t0) REVERT: F 147 LYS cc_start: 0.8008 (pttm) cc_final: 0.7797 (mtmt) REVERT: F 151 LYS cc_start: 0.6629 (mmmt) cc_final: 0.6357 (mmtt) REVERT: F 184 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: F 197 THR cc_start: 0.9005 (m) cc_final: 0.8796 (m) REVERT: G 45 ASP cc_start: 0.7990 (t70) cc_final: 0.7055 (t0) REVERT: G 195 MET cc_start: 0.8375 (tpt) cc_final: 0.8001 (tpt) REVERT: G 256 MET cc_start: 0.8278 (mtm) cc_final: 0.8040 (mtt) outliers start: 68 outliers final: 19 residues processed: 480 average time/residue: 0.5754 time to fit residues: 316.6590 Evaluate side-chains 451 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 423 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 147 LYS Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 192 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 217 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 115 optimal weight: 0.4980 chunk 261 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 280 GLN J 177 GLN Z 3 ASN Z 51 GLN D 361 GLN E 176 HIS E 203 GLN E 209 ASN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN G 31 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.100922 restraints weight = 27422.378| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.18 r_work: 0.2553 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.458 24985 Z= 0.215 Angle : 0.791 33.485 34162 Z= 0.332 Chirality : 0.045 0.289 3592 Planarity : 0.005 0.056 4244 Dihedral : 12.018 127.425 3677 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.68 % Allowed : 17.96 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.77 (0.15), residues: 2972 helix: 1.08 (0.13), residues: 1657 sheet: -2.24 (0.58), residues: 54 loop : 0.02 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 10 TYR 0.020 0.002 TYR J 221 PHE 0.023 0.002 PHE I 255 TRP 0.020 0.002 TRP D 147 HIS 0.010 0.002 HIS I 87 Details of bonding type rmsd covalent geometry : bond 0.00503 (24942) covalent geometry : angle 0.73849 (34151) SS BOND : bond 0.00799 ( 1) SS BOND : angle 3.00146 ( 2) hydrogen bonds : bond 0.05101 ( 1302) hydrogen bonds : angle 5.27920 ( 3741) metal coordination : bond 0.02292 ( 9) metal coordination : angle 17.45216 ( 9) Misc. bond : bond 0.19207 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 449 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8621 (tp-100) REVERT: J 34 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8669 (mt) REVERT: J 253 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.8003 (ptm-80) REVERT: J 255 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7167 (t80) REVERT: K 28 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: Z 75 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8801 (m) REVERT: Z 76 HIS cc_start: 0.8582 (t-90) cc_final: 0.8231 (t-90) REVERT: Z 147 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.7952 (mtpp) REVERT: D 3 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6580 (mppt) REVERT: D 308 MET cc_start: 0.8981 (tpt) cc_final: 0.8723 (tpp) REVERT: N 95 TYR cc_start: 0.9186 (t80) cc_final: 0.8837 (t80) REVERT: E 238 TYR cc_start: 0.7000 (t80) cc_final: 0.6711 (t80) REVERT: E 412 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8032 (ttm170) REVERT: E 452 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8143 (ttp) REVERT: F 24 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7666 (mp) REVERT: F 127 ASN cc_start: 0.8822 (t0) cc_final: 0.8570 (t0) REVERT: F 151 LYS cc_start: 0.6682 (mmmt) cc_final: 0.6371 (mmtt) REVERT: F 184 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: G 45 ASP cc_start: 0.8301 (t70) cc_final: 0.7383 (t0) REVERT: G 83 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8397 (ptpp) REVERT: G 195 MET cc_start: 0.8438 (tpt) cc_final: 0.8003 (tpt) REVERT: G 256 MET cc_start: 0.8375 (mtm) cc_final: 0.8156 (mtt) REVERT: G 269 TYR cc_start: 0.8899 (m-80) cc_final: 0.8583 (m-10) outliers start: 88 outliers final: 35 residues processed: 490 average time/residue: 0.6005 time to fit residues: 336.5361 Evaluate side-chains 473 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 427 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 253 ARG Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 147 LYS Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 192 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 150 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102484 restraints weight = 27731.161| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.19 r_work: 0.2604 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.430 24985 Z= 0.161 Angle : 0.731 29.391 34162 Z= 0.308 Chirality : 0.043 0.259 3592 Planarity : 0.005 0.055 4244 Dihedral : 11.624 126.110 3677 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.60 % Allowed : 18.63 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.86 (0.15), residues: 2972 helix: 1.16 (0.13), residues: 1663 sheet: -2.24 (0.60), residues: 54 loop : 0.03 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 10 TYR 0.027 0.002 TYR M 240 PHE 0.022 0.002 PHE I 255 TRP 0.019 0.001 TRP C 146 HIS 0.008 0.001 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00375 (24942) covalent geometry : angle 0.68732 (34151) SS BOND : bond 0.00399 ( 1) SS BOND : angle 1.87981 ( 2) hydrogen bonds : bond 0.04605 ( 1302) hydrogen bonds : angle 5.10849 ( 3741) metal coordination : bond 0.01803 ( 9) metal coordination : angle 15.28733 ( 9) Misc. bond : bond 0.17300 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 443 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8500 (tp40) REVERT: J 34 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8647 (mt) REVERT: J 255 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6902 (t80) REVERT: K 28 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: Z 75 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8820 (m) REVERT: Z 76 HIS cc_start: 0.8557 (t-90) cc_final: 0.8220 (t-90) REVERT: Z 147 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.7970 (mtpp) REVERT: Z 161 LEU cc_start: 0.9040 (mt) cc_final: 0.8714 (mt) REVERT: D 3 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6538 (mppt) REVERT: D 280 GLN cc_start: 0.8720 (mt0) cc_final: 0.8473 (mt0) REVERT: D 308 MET cc_start: 0.9004 (tpt) cc_final: 0.8755 (tpp) REVERT: N 28 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: N 95 TYR cc_start: 0.9147 (t80) cc_final: 0.8838 (t80) REVERT: E 261 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.7944 (m-70) REVERT: E 371 TYR cc_start: 0.8082 (m-80) cc_final: 0.7701 (m-80) REVERT: E 412 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.8041 (ttm170) REVERT: E 438 ARG cc_start: 0.8477 (ttm170) cc_final: 0.8253 (tmm-80) REVERT: E 452 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8192 (ttp) REVERT: E 462 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6890 (pp30) REVERT: F 24 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7566 (mp) REVERT: F 127 ASN cc_start: 0.8763 (t0) cc_final: 0.8518 (t0) REVERT: F 151 LYS cc_start: 0.6655 (mmmt) cc_final: 0.6296 (mmtt) REVERT: F 170 GLU cc_start: 0.8046 (mp0) cc_final: 0.7649 (mp0) REVERT: F 184 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: G 40 VAL cc_start: 0.4255 (t) cc_final: 0.3974 (m) REVERT: G 45 ASP cc_start: 0.8345 (t70) cc_final: 0.7491 (t0) REVERT: G 73 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8076 (tp) REVERT: G 83 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8402 (ptpp) REVERT: G 195 MET cc_start: 0.8385 (tpt) cc_final: 0.7885 (tpt) REVERT: G 269 TYR cc_start: 0.8926 (m-80) cc_final: 0.8688 (m-10) outliers start: 86 outliers final: 29 residues processed: 486 average time/residue: 0.6006 time to fit residues: 335.0425 Evaluate side-chains 454 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 411 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 147 LYS Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 28 GLN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 192 HIS Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 134 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 196 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 253 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN Z 62 GLN ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.102543 restraints weight = 27589.628| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.14 r_work: 0.2629 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.426 24985 Z= 0.162 Angle : 0.722 27.482 34162 Z= 0.307 Chirality : 0.043 0.307 3592 Planarity : 0.005 0.053 4244 Dihedral : 11.384 121.149 3677 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.52 % Allowed : 18.79 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.90 (0.15), residues: 2972 helix: 1.22 (0.13), residues: 1652 sheet: -2.27 (0.60), residues: 54 loop : 0.03 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 10 TYR 0.024 0.002 TYR C 105 PHE 0.020 0.002 PHE I 95 TRP 0.017 0.001 TRP D 147 HIS 0.010 0.001 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00379 (24942) covalent geometry : angle 0.68471 (34151) SS BOND : bond 0.00196 ( 1) SS BOND : angle 3.24865 ( 2) hydrogen bonds : bond 0.04582 ( 1302) hydrogen bonds : angle 5.06887 ( 3741) metal coordination : bond 0.01720 ( 9) metal coordination : angle 14.13559 ( 9) Misc. bond : bond 0.17269 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 435 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8491 (tp40) REVERT: J 34 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8657 (mt) REVERT: J 132 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8733 (mt-10) REVERT: J 255 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6861 (t80) REVERT: Z 76 HIS cc_start: 0.8536 (t-90) cc_final: 0.8173 (t-90) REVERT: Z 161 LEU cc_start: 0.9150 (mt) cc_final: 0.8886 (mt) REVERT: D 3 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6519 (mppt) REVERT: D 280 GLN cc_start: 0.8733 (mt0) cc_final: 0.8521 (mt0) REVERT: D 308 MET cc_start: 0.9005 (tpt) cc_final: 0.8768 (tpp) REVERT: M 255 TYR cc_start: 0.9099 (m-80) cc_final: 0.8874 (m-80) REVERT: N 95 TYR cc_start: 0.9146 (t80) cc_final: 0.8827 (t80) REVERT: E 261 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.8015 (m-70) REVERT: E 371 TYR cc_start: 0.8178 (m-80) cc_final: 0.7759 (m-80) REVERT: E 375 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7937 (ptmm) REVERT: E 412 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7960 (ttm170) REVERT: E 452 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8179 (ttp) REVERT: F 24 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7584 (mp) REVERT: F 127 ASN cc_start: 0.8755 (t0) cc_final: 0.8507 (t0) REVERT: F 151 LYS cc_start: 0.6570 (mmmt) cc_final: 0.6286 (mmtt) REVERT: F 184 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: G 31 GLN cc_start: 0.8503 (mt0) cc_final: 0.8289 (mt0) REVERT: G 40 VAL cc_start: 0.4450 (t) cc_final: 0.4210 (m) REVERT: G 73 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8193 (tp) REVERT: G 83 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8431 (ptpp) REVERT: G 195 MET cc_start: 0.8320 (tpt) cc_final: 0.7772 (tpt) REVERT: G 208 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8330 (ttpp) REVERT: G 269 TYR cc_start: 0.8976 (m-80) cc_final: 0.8753 (m-10) outliers start: 84 outliers final: 38 residues processed: 481 average time/residue: 0.5929 time to fit residues: 327.6245 Evaluate side-chains 462 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 415 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 192 HIS Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 118 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 8 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN J 90 HIS K 113 GLN L 38 GLN Z 3 ASN Z 51 GLN N 113 GLN E 63 ASN E 203 GLN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103844 restraints weight = 27739.201| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.11 r_work: 0.2625 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.420 24985 Z= 0.144 Angle : 0.710 26.203 34162 Z= 0.301 Chirality : 0.043 0.314 3592 Planarity : 0.004 0.054 4244 Dihedral : 10.970 113.734 3677 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.89 % Allowed : 19.59 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.97 (0.15), residues: 2972 helix: 1.29 (0.13), residues: 1648 sheet: -2.42 (0.57), residues: 54 loop : 0.05 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 10 TYR 0.024 0.002 TYR M 240 PHE 0.020 0.001 PHE I 255 TRP 0.016 0.001 TRP D 147 HIS 0.010 0.001 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00336 (24942) covalent geometry : angle 0.67424 (34151) SS BOND : bond 0.00529 ( 1) SS BOND : angle 2.80607 ( 2) hydrogen bonds : bond 0.04379 ( 1302) hydrogen bonds : angle 4.99710 ( 3741) metal coordination : bond 0.01584 ( 9) metal coordination : angle 13.60040 ( 9) Misc. bond : bond 0.16245 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 441 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LEU cc_start: 0.7117 (mt) cc_final: 0.6442 (tt) REVERT: I 150 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8465 (tp40) REVERT: J 34 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8632 (mt) REVERT: J 255 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6822 (t80) REVERT: K 28 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: D 3 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.6517 (mppt) REVERT: D 280 GLN cc_start: 0.8759 (mt0) cc_final: 0.8463 (mt0) REVERT: D 308 MET cc_start: 0.8976 (tpt) cc_final: 0.8745 (tpp) REVERT: N 95 TYR cc_start: 0.9133 (t80) cc_final: 0.8836 (t80) REVERT: E 261 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8036 (m-70) REVERT: E 371 TYR cc_start: 0.8154 (m-80) cc_final: 0.7698 (m-80) REVERT: E 375 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8046 (ptmm) REVERT: E 412 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7966 (ttm170) REVERT: E 452 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8178 (ttp) REVERT: F 24 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7475 (mp) REVERT: F 37 ASP cc_start: 0.7792 (p0) cc_final: 0.7477 (p0) REVERT: F 108 ASP cc_start: 0.8227 (t70) cc_final: 0.7947 (t70) REVERT: F 151 LYS cc_start: 0.6595 (mmmt) cc_final: 0.6326 (mmtt) REVERT: F 169 ASP cc_start: 0.8186 (m-30) cc_final: 0.7870 (m-30) REVERT: F 170 GLU cc_start: 0.7965 (mp0) cc_final: 0.7434 (mp0) REVERT: F 184 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: G 31 GLN cc_start: 0.8544 (mt0) cc_final: 0.8333 (mt0) REVERT: G 83 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8419 (ptpp) REVERT: G 114 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7620 (mtpp) REVERT: G 195 MET cc_start: 0.8273 (tpt) cc_final: 0.7665 (tpt) REVERT: G 208 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8416 (ttpp) REVERT: G 269 TYR cc_start: 0.8959 (m-80) cc_final: 0.8746 (m-10) outliers start: 69 outliers final: 35 residues processed: 474 average time/residue: 0.6100 time to fit residues: 330.3502 Evaluate side-chains 482 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 438 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 192 HIS Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 278 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 193 optimal weight: 2.9990 chunk 228 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 119 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN L 38 GLN Z 3 ASN Z 51 GLN E 63 ASN E 203 GLN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.103259 restraints weight = 27746.263| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.14 r_work: 0.2602 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.417 24985 Z= 0.160 Angle : 0.715 24.928 34162 Z= 0.306 Chirality : 0.043 0.285 3592 Planarity : 0.004 0.054 4244 Dihedral : 10.617 120.162 3677 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.14 % Allowed : 19.84 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.93 (0.15), residues: 2972 helix: 1.22 (0.13), residues: 1665 sheet: -2.45 (0.56), residues: 54 loop : 0.06 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 253 TYR 0.025 0.002 TYR M 240 PHE 0.019 0.002 PHE I 95 TRP 0.016 0.001 TRP D 147 HIS 0.006 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00374 (24942) covalent geometry : angle 0.68425 (34151) SS BOND : bond 0.00462 ( 1) SS BOND : angle 2.71684 ( 2) hydrogen bonds : bond 0.04497 ( 1302) hydrogen bonds : angle 4.99367 ( 3741) metal coordination : bond 0.01542 ( 9) metal coordination : angle 12.82059 ( 9) Misc. bond : bond 0.16885 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 453 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6496 (tm-30) REVERT: C 127 LEU cc_start: 0.7132 (mt) cc_final: 0.6477 (tt) REVERT: I 150 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8508 (tp40) REVERT: I 297 TYR cc_start: 0.9012 (t80) cc_final: 0.8622 (t80) REVERT: J 34 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8473 (mt) REVERT: J 255 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6978 (t80) REVERT: L 34 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7782 (mmtm) REVERT: Z 169 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7713 (mm-40) REVERT: D 3 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6511 (mppt) REVERT: D 280 GLN cc_start: 0.8772 (mt0) cc_final: 0.8521 (mt0) REVERT: D 308 MET cc_start: 0.8984 (tpt) cc_final: 0.8760 (tpp) REVERT: N 95 TYR cc_start: 0.9148 (t80) cc_final: 0.8830 (t80) REVERT: E 261 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.8076 (m-70) REVERT: E 371 TYR cc_start: 0.8281 (m-80) cc_final: 0.7773 (m-80) REVERT: E 375 LYS cc_start: 0.8331 (ttpp) cc_final: 0.8108 (ptmm) REVERT: E 412 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.7960 (ttm170) REVERT: E 462 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6861 (pp30) REVERT: F 24 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7832 (mp) REVERT: F 37 ASP cc_start: 0.7892 (p0) cc_final: 0.6502 (t70) REVERT: F 108 ASP cc_start: 0.8227 (t70) cc_final: 0.8009 (t70) REVERT: F 184 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: G 83 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8432 (ptpp) REVERT: G 114 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7794 (mtpp) REVERT: G 195 MET cc_start: 0.8279 (tpt) cc_final: 0.7657 (tpt) REVERT: G 208 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8334 (ttpp) REVERT: G 269 TYR cc_start: 0.8979 (m-80) cc_final: 0.8758 (m-10) outliers start: 75 outliers final: 43 residues processed: 491 average time/residue: 0.5667 time to fit residues: 318.9080 Evaluate side-chains 480 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 427 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 278 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 145 optimal weight: 0.5980 chunk 218 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN E 63 ASN E 203 GLN ** E 244 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 = 0.3647 r_free = 0.3647 target = 0.145864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103060 restraints weight = 27685.832| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.12 r_work: 0.2637 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.414 24985 Z= 0.159 Angle : 0.805 45.034 34162 Z= 0.315 Chirality : 0.043 0.308 3592 Planarity : 0.005 0.056 4244 Dihedral : 10.466 118.829 3675 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.85 % Allowed : 20.64 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.89 (0.15), residues: 2972 helix: 1.21 (0.13), residues: 1671 sheet: -2.38 (0.54), residues: 57 loop : 0.03 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 10 TYR 0.029 0.002 TYR G 72 PHE 0.020 0.002 PHE C 151 TRP 0.016 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00370 (24942) covalent geometry : angle 0.69475 (34151) SS BOND : bond 0.00099 ( 1) SS BOND : angle 2.52587 ( 2) hydrogen bonds : bond 0.04470 ( 1302) hydrogen bonds : angle 4.99684 ( 3741) metal coordination : bond 0.04498 ( 9) metal coordination : angle 24.97657 ( 9) Misc. bond : bond 0.16571 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 439 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8536 (tp40) REVERT: I 297 TYR cc_start: 0.8971 (t80) cc_final: 0.8655 (t80) REVERT: J 34 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8297 (mt) REVERT: J 255 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6977 (t80) REVERT: K 28 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: L 34 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7776 (mmtm) REVERT: Z 169 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7664 (mm-40) REVERT: D 3 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6514 (mppt) REVERT: D 308 MET cc_start: 0.8991 (tpt) cc_final: 0.8788 (tpp) REVERT: N 95 TYR cc_start: 0.9152 (t80) cc_final: 0.8827 (t80) REVERT: E 261 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8018 (m-70) REVERT: E 371 TYR cc_start: 0.8292 (m-80) cc_final: 0.7820 (m-80) REVERT: E 375 LYS cc_start: 0.8306 (ttpp) cc_final: 0.8065 (ptmm) REVERT: E 412 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7914 (ttm170) REVERT: E 462 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6799 (pp30) REVERT: F 24 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7884 (mp) REVERT: F 37 ASP cc_start: 0.7905 (p0) cc_final: 0.6516 (t70) REVERT: F 184 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: G 83 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8443 (ptpp) REVERT: G 195 MET cc_start: 0.8213 (tpt) cc_final: 0.7682 (tpt) REVERT: G 208 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8297 (ttpp) outliers start: 68 outliers final: 36 residues processed: 471 average time/residue: 0.5917 time to fit residues: 319.1271 Evaluate side-chains 486 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 439 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 278 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 219 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 184 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 237 optimal weight: 0.9980 chunk 286 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN E 203 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103233 restraints weight = 27678.581| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.10 r_work: 0.2619 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.415 24985 Z= 0.155 Angle : 0.803 43.255 34162 Z= 0.315 Chirality : 0.043 0.329 3592 Planarity : 0.005 0.061 4244 Dihedral : 10.393 114.717 3675 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.34 % Allowed : 21.10 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.89 (0.15), residues: 2972 helix: 1.22 (0.13), residues: 1664 sheet: -2.42 (0.53), residues: 57 loop : 0.01 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 10 TYR 0.030 0.002 TYR G 72 PHE 0.018 0.002 PHE I 255 TRP 0.016 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00363 (24942) covalent geometry : angle 0.69645 (34151) SS BOND : bond 0.00164 ( 1) SS BOND : angle 2.49544 ( 2) hydrogen bonds : bond 0.04432 ( 1302) hydrogen bonds : angle 4.98596 ( 3741) metal coordination : bond 0.03182 ( 9) metal coordination : angle 24.64609 ( 9) Misc. bond : bond 0.16681 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 448 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6501 (tm-30) REVERT: I 150 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8479 (tp40) REVERT: I 297 TYR cc_start: 0.8944 (t80) cc_final: 0.8647 (t80) REVERT: J 34 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8139 (mt) REVERT: J 255 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6869 (t80) REVERT: L 34 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7732 (mmtm) REVERT: Z 169 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7654 (mm-40) REVERT: D 3 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6469 (mppt) REVERT: D 280 GLN cc_start: 0.8767 (mt0) cc_final: 0.8485 (mt0) REVERT: D 308 MET cc_start: 0.8944 (tpt) cc_final: 0.8738 (tpp) REVERT: N 95 TYR cc_start: 0.9128 (t80) cc_final: 0.8799 (t80) REVERT: E 203 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8745 (tp-100) REVERT: E 261 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8019 (m-70) REVERT: E 371 TYR cc_start: 0.8283 (m-80) cc_final: 0.7765 (m-80) REVERT: E 375 LYS cc_start: 0.8302 (ttpp) cc_final: 0.8062 (ptmm) REVERT: E 412 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7838 (ttm170) REVERT: E 462 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6728 (pp30) REVERT: F 24 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7874 (mp) REVERT: F 37 ASP cc_start: 0.7911 (p0) cc_final: 0.6523 (t70) REVERT: F 170 GLU cc_start: 0.8034 (mp0) cc_final: 0.7539 (mp0) REVERT: F 184 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: G 83 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8421 (ptpp) REVERT: G 195 MET cc_start: 0.8200 (tpt) cc_final: 0.7655 (tpt) REVERT: G 208 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8304 (ttpp) outliers start: 56 outliers final: 35 residues processed: 476 average time/residue: 0.6135 time to fit residues: 333.7900 Evaluate side-chains 465 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 419 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 278 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 33 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 161 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 128 optimal weight: 0.9990 chunk 249 optimal weight: 0.0370 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN F 124 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.104436 restraints weight = 27861.656| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.14 r_work: 0.2640 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.412 24985 Z= 0.140 Angle : 0.797 42.874 34162 Z= 0.314 Chirality : 0.043 0.326 3592 Planarity : 0.005 0.057 4244 Dihedral : 10.275 112.191 3675 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.18 % Allowed : 21.47 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.94 (0.15), residues: 2972 helix: 1.27 (0.13), residues: 1661 sheet: -2.41 (0.53), residues: 57 loop : 0.02 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 10 TYR 0.026 0.002 TYR M 240 PHE 0.019 0.001 PHE I 255 TRP 0.016 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00328 (24942) covalent geometry : angle 0.69071 (34151) SS BOND : bond 0.00186 ( 1) SS BOND : angle 2.44915 ( 2) hydrogen bonds : bond 0.04295 ( 1302) hydrogen bonds : angle 4.95885 ( 3741) metal coordination : bond 0.02962 ( 9) metal coordination : angle 24.46505 ( 9) Misc. bond : bond 0.15619 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 427 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6447 (tm-30) REVERT: I 150 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8496 (tp40) REVERT: I 297 TYR cc_start: 0.8956 (t80) cc_final: 0.8615 (t80) REVERT: J 34 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7849 (mt) REVERT: J 255 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6760 (t80) REVERT: D 3 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6498 (mppt) REVERT: D 280 GLN cc_start: 0.8764 (mt0) cc_final: 0.8455 (mt0) REVERT: N 95 TYR cc_start: 0.9143 (t80) cc_final: 0.8851 (t80) REVERT: E 261 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.8036 (m-70) REVERT: E 371 TYR cc_start: 0.8304 (m-80) cc_final: 0.7809 (m-80) REVERT: E 375 LYS cc_start: 0.8286 (ttpp) cc_final: 0.8064 (ptmm) REVERT: E 412 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7832 (ttm170) REVERT: E 462 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6706 (pp30) REVERT: F 24 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7900 (mp) REVERT: F 37 ASP cc_start: 0.7919 (p0) cc_final: 0.6547 (t70) REVERT: F 184 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: G 8 TYR cc_start: 0.7829 (t80) cc_final: 0.7621 (t80) REVERT: G 83 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8350 (ptpp) REVERT: G 195 MET cc_start: 0.8142 (tpt) cc_final: 0.7620 (tpt) REVERT: G 208 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8339 (ttpp) outliers start: 52 outliers final: 32 residues processed: 454 average time/residue: 0.5937 time to fit residues: 307.8598 Evaluate side-chains 462 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 422 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 278 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 217 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 255 optimal weight: 0.0670 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN D 361 GLN E 203 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.103566 restraints weight = 27801.788| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.14 r_work: 0.2633 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.427 24985 Z= 0.161 Angle : 0.820 42.009 34162 Z= 0.321 Chirality : 0.044 0.401 3592 Planarity : 0.005 0.056 4244 Dihedral : 10.317 108.760 3675 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.39 % Allowed : 21.35 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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 aren not related in a simple way. whole: 0.93 (0.15), residues: 2972 helix: 1.25 (0.13), residues: 1661 sheet: -2.32 (0.53), residues: 56 loop : 0.01 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 253 TYR 0.027 0.002 TYR M 240 PHE 0.018 0.002 PHE I 95 TRP 0.015 0.001 TRP D 54 HIS 0.007 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00375 (24942) covalent geometry : angle 0.71813 (34151) SS BOND : bond 0.00239 ( 1) SS BOND : angle 2.52157 ( 2) hydrogen bonds : bond 0.04449 ( 1302) hydrogen bonds : angle 4.97557 ( 3741) metal coordination : bond 0.02753 ( 9) metal coordination : angle 24.31699 ( 9) Misc. bond : bond 0.17604 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9521.70 seconds wall clock time: 162 minutes 24.23 seconds (9744.23 seconds total)