Starting phenix.real_space_refine on Fri May 23 19:40:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smr_40601/05_2025/8smr_40601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smr_40601/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8smr_40601/05_2025/8smr_40601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smr_40601/05_2025/8smr_40601.map" model { file = "/net/cci-nas-00/data/ceres_data/8smr_40601/05_2025/8smr_40601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smr_40601/05_2025/8smr_40601.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} 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: 13.19, per 1000 atoms: 0.55 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: 6.64 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.14 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: 7.65 Time building geometry restraints manager: 7.36 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 403 or resid 501 through 503)) } ncs_group { reference = (chain 'J' and (resid 26 through 163 or resid 193 through 257 or resid 500)) selection = (chain 'M' and (resid 26 through 257 or resid 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 55.680 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.860 ------------------------------------------------------------------------------- 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 : 9.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (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 TRP 0.015 0.001 TRP I 54 HIS 0.013 0.001 HIS Z 158 PHE 0.024 0.001 PHE I 255 TYR 0.014 0.001 TYR I 388 ARG 0.014 0.000 ARG J 253 Details of bonding type rmsd hydrogen bonds : bond 0.13827 ( 1302) hydrogen bonds : angle 6.54112 ( 3741) metal coordination : bond 0.01173 ( 9) metal coordination : angle 20.06080 ( 9) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.27200 ( 2) covalent geometry : bond 0.00752 (24942) covalent geometry : angle 0.84181 (34151) 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 : 2.572 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: 1.3231 time to fit residues: 715.1157 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 : 2.785 ------------------------------------------------------------------------------- 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 249 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 232 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 172 optimal weight: 0.0050 chunk 268 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.147794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.104185 restraints weight = 27341.929| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.07 r_work: 0.2656 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.424 24985 Z= 0.164 Angle : 0.785 36.035 34162 Z= 0.327 Chirality : 0.044 0.242 3592 Planarity : 0.005 0.051 4244 Dihedral : 12.236 129.009 3696 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.76 % Allowed : 18.17 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 2972 helix: 1.13 (0.13), residues: 1656 sheet: -2.33 (0.69), residues: 42 loop : 0.07 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 147 HIS 0.008 0.001 HIS E 300 PHE 0.028 0.002 PHE I 255 TYR 0.024 0.002 TYR C 105 ARG 0.008 0.001 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04928 ( 1302) hydrogen bonds : angle 5.36390 ( 3741) metal coordination : bond 0.02222 ( 9) metal coordination : angle 18.79153 ( 9) SS BOND : bond 0.00001 ( 1) SS BOND : angle 2.01042 ( 2) covalent geometry : bond 0.00376 (24942) covalent geometry : angle 0.72293 (34151) Misc. bond : bond 0.16919 ( 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 513 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 447 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8615 (mt) REVERT: J 52 MET cc_start: 0.9003 (mtp) cc_final: 0.8794 (mtm) REVERT: K 28 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: Z 75 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8758 (m) REVERT: Z 76 HIS cc_start: 0.8516 (t-90) cc_final: 0.8196 (t-90) REVERT: Z 164 ARG cc_start: 0.8612 (mtm180) cc_final: 0.8266 (mtm180) REVERT: D 3 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6560 (mppt) REVERT: D 308 MET cc_start: 0.8872 (tpt) cc_final: 0.8626 (tpp) REVERT: N 95 TYR cc_start: 0.9145 (t80) cc_final: 0.8866 (t80) REVERT: E 229 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8481 (mmmt) REVERT: E 239 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7523 (mmm-85) REVERT: E 252 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5985 (m-10) REVERT: E 410 MET cc_start: 0.8464 (mmm) cc_final: 0.8255 (mtm) REVERT: F 24 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7480 (mp) REVERT: F 127 ASN cc_start: 0.8774 (t0) cc_final: 0.8504 (t0) REVERT: F 151 LYS cc_start: 0.6586 (mmmt) cc_final: 0.6324 (mmtt) REVERT: F 182 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7704 (ptpt) REVERT: F 184 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: F 197 THR cc_start: 0.9008 (m) cc_final: 0.8804 (m) REVERT: G 45 ASP cc_start: 0.7972 (t70) cc_final: 0.7016 (t0) REVERT: G 195 MET cc_start: 0.8375 (tpt) cc_final: 0.7957 (tpt) REVERT: G 256 MET cc_start: 0.8258 (mtm) cc_final: 0.8021 (mtt) outliers start: 66 outliers final: 18 residues processed: 481 average time/residue: 1.3191 time to fit residues: 728.2509 Evaluate side-chains 455 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 429 time to evaluate : 2.379 ------------------------------------------------------------------------------- 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 Z residue 75 VAL 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 252 TYR 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 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 73 LEU 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 113 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 287 optimal weight: 20.0000 chunk 184 optimal weight: 0.0060 chunk 110 optimal weight: 5.9990 chunk 182 optimal weight: 0.0270 chunk 291 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 overall best weight: 0.6014 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 ASN Z 51 GLN D 361 GLN E 209 ASN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS G 31 GLN ** 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 = 0.3670 r_free = 0.3670 target = 0.147885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104225 restraints weight = 27266.358| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.13 r_work: 0.2664 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1478 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= 0.150 Angle : 0.729 30.958 34162 Z= 0.305 Chirality : 0.043 0.257 3592 Planarity : 0.005 0.050 4244 Dihedral : 11.711 127.798 3677 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.52 % Allowed : 18.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 2972 helix: 1.22 (0.13), residues: 1658 sheet: -2.19 (0.59), residues: 54 loop : 0.05 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 147 HIS 0.007 0.001 HIS E 300 PHE 0.023 0.001 PHE I 255 TYR 0.020 0.002 TYR D 388 ARG 0.008 0.000 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 1302) hydrogen bonds : angle 5.14827 ( 3741) metal coordination : bond 0.01847 ( 9) metal coordination : angle 16.11246 ( 9) SS BOND : bond 0.01708 ( 1) SS BOND : angle 2.12538 ( 2) covalent geometry : bond 0.00344 (24942) covalent geometry : angle 0.68042 (34151) Misc. bond : bond 0.16322 ( 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 544 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 460 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8393 (tp40) REVERT: J 34 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8630 (mt) REVERT: K 23 ASP cc_start: 0.8308 (t0) cc_final: 0.7999 (t70) REVERT: K 28 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: Z 75 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8780 (m) REVERT: Z 76 HIS cc_start: 0.8522 (t-90) cc_final: 0.8138 (t-90) REVERT: Z 147 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.7957 (mtpp) REVERT: D 3 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.6592 (mppt) REVERT: D 74 MET cc_start: 0.9075 (mmm) cc_final: 0.8860 (mmm) REVERT: D 308 MET cc_start: 0.8896 (tpt) cc_final: 0.8623 (tpp) REVERT: N 95 TYR cc_start: 0.9130 (t80) cc_final: 0.8791 (t80) REVERT: E 229 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8424 (mmmt) REVERT: E 412 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7899 (ttm170) REVERT: E 462 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7175 (pt0) REVERT: F 24 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7583 (mp) REVERT: F 127 ASN cc_start: 0.8791 (t0) cc_final: 0.8521 (t0) REVERT: F 151 LYS cc_start: 0.6607 (mmmt) cc_final: 0.6193 (mmtt) REVERT: F 184 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: G 45 ASP cc_start: 0.8202 (t70) cc_final: 0.7260 (t0) REVERT: G 83 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8223 (ptpp) REVERT: G 195 MET cc_start: 0.8316 (tpt) cc_final: 0.7839 (tpt) REVERT: G 256 MET cc_start: 0.8242 (mtm) cc_final: 0.8034 (mtt) REVERT: G 269 TYR cc_start: 0.8783 (m-80) cc_final: 0.8503 (m-10) outliers start: 84 outliers final: 28 residues processed: 497 average time/residue: 1.3138 time to fit residues: 750.8872 Evaluate side-chains 458 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 421 time to evaluate : 2.641 ------------------------------------------------------------------------------- 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 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 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 E residue 35 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 371 TYR 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 87 SER 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 144 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 261 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN ** J 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN Z 3 ASN Z 51 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104150 restraints weight = 27920.783| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.17 r_work: 0.2615 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1700 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= 0.164 Angle : 0.732 28.337 34162 Z= 0.309 Chirality : 0.044 0.292 3592 Planarity : 0.005 0.050 4244 Dihedral : 11.497 125.608 3677 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.39 % Allowed : 18.96 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 2972 helix: 1.22 (0.13), residues: 1652 sheet: -2.29 (0.59), residues: 54 loop : 0.04 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 147 HIS 0.008 0.001 HIS C 76 PHE 0.021 0.002 PHE I 255 TYR 0.024 0.002 TYR M 240 ARG 0.009 0.000 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 1302) hydrogen bonds : angle 5.07266 ( 3741) metal coordination : bond 0.01718 ( 9) metal coordination : angle 14.46790 ( 9) SS BOND : bond 0.01247 ( 1) SS BOND : angle 4.95631 ( 2) covalent geometry : bond 0.00383 (24942) covalent geometry : angle 0.69204 (34151) Misc. bond : bond 0.16894 ( 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 520 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 439 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8423 (tp40) REVERT: J 34 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8643 (mt) REVERT: J 255 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6909 (t80) REVERT: Z 75 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8882 (m) REVERT: Z 76 HIS cc_start: 0.8529 (t-90) cc_final: 0.8132 (t-90) REVERT: Z 114 LYS cc_start: 0.8219 (mttt) cc_final: 0.7945 (ptpt) REVERT: Z 147 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.7992 (mtpp) REVERT: D 3 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6549 (mppt) REVERT: D 74 MET cc_start: 0.9124 (mmm) cc_final: 0.8897 (mmm) REVERT: D 308 MET cc_start: 0.9002 (tpt) cc_final: 0.8752 (tpp) REVERT: N 95 TYR cc_start: 0.9164 (t80) cc_final: 0.8858 (t80) REVERT: E 261 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.7786 (m-70) REVERT: E 412 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8007 (ttm170) REVERT: E 452 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8226 (ttp) REVERT: F 24 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7184 (mp) REVERT: F 127 ASN cc_start: 0.8782 (t0) cc_final: 0.8525 (t0) REVERT: F 151 LYS cc_start: 0.6547 (mmmt) cc_final: 0.6301 (mmtt) REVERT: F 184 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: G 31 GLN cc_start: 0.8359 (mt0) cc_final: 0.8126 (mt0) REVERT: G 45 ASP cc_start: 0.8269 (t70) cc_final: 0.7585 (t70) REVERT: G 83 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8348 (ptpp) REVERT: G 195 MET cc_start: 0.8260 (tpt) cc_final: 0.7754 (tpt) REVERT: G 269 TYR cc_start: 0.8900 (m-80) cc_final: 0.8647 (m-10) outliers start: 81 outliers final: 32 residues processed: 475 average time/residue: 1.3617 time to fit residues: 743.1013 Evaluate side-chains 458 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 416 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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 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 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 135 MET 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 167 SER 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 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 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 174 optimal weight: 0.9990 chunk 163 optimal weight: 0.0370 chunk 118 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 168 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 217 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 ** J 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Z 3 ASN Z 51 GLN Z 62 GLN N 201 HIS ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS ** 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 = 0.3659 r_free = 0.3659 target = 0.146855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.103587 restraints weight = 27903.192| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.15 r_work: 0.2629 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.413 24985 Z= 0.148 Angle : 0.710 26.443 34162 Z= 0.301 Chirality : 0.043 0.278 3592 Planarity : 0.004 0.050 4244 Dihedral : 11.215 120.893 3677 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.01 % Allowed : 19.84 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 2972 helix: 1.27 (0.13), residues: 1654 sheet: -2.30 (0.58), residues: 57 loop : 0.03 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 147 HIS 0.012 0.001 HIS C 76 PHE 0.020 0.001 PHE I 255 TYR 0.024 0.002 TYR M 240 ARG 0.008 0.000 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 1302) hydrogen bonds : angle 5.01173 ( 3741) metal coordination : bond 0.01532 ( 9) metal coordination : angle 13.54352 ( 9) SS BOND : bond 0.00502 ( 1) SS BOND : angle 3.54870 ( 2) covalent geometry : bond 0.00347 (24942) covalent geometry : angle 0.67516 (34151) Misc. bond : bond 0.16155 ( 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 507 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 435 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8402 (tp40) REVERT: J 34 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8597 (mt) REVERT: J 189 GLU cc_start: 0.7274 (tp30) cc_final: 0.6795 (tp30) REVERT: J 255 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6839 (t80) REVERT: K 28 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: Z 76 HIS cc_start: 0.8542 (t-90) cc_final: 0.8186 (t-90) REVERT: Z 114 LYS cc_start: 0.8216 (mttt) cc_final: 0.7902 (ptpt) REVERT: D 3 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6537 (mppt) REVERT: D 74 MET cc_start: 0.9116 (mmm) cc_final: 0.8888 (mmm) REVERT: D 308 MET cc_start: 0.8983 (tpt) cc_final: 0.8744 (tpp) REVERT: N 95 TYR cc_start: 0.9143 (t80) cc_final: 0.8850 (t80) REVERT: E 261 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7832 (m-70) REVERT: E 412 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.7999 (ttm170) REVERT: E 452 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8279 (ttp) REVERT: E 462 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6903 (pp30) REVERT: F 24 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7794 (mp) REVERT: F 127 ASN cc_start: 0.8761 (t0) cc_final: 0.8512 (t0) REVERT: F 151 LYS cc_start: 0.6553 (mmmt) cc_final: 0.6288 (mmtt) REVERT: F 184 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: G 31 GLN cc_start: 0.8489 (mt0) cc_final: 0.8278 (mt0) REVERT: G 40 VAL cc_start: 0.4046 (t) cc_final: 0.3805 (m) REVERT: G 83 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8396 (ptpp) REVERT: G 195 MET cc_start: 0.8217 (tpt) cc_final: 0.7645 (tpt) REVERT: G 269 TYR cc_start: 0.8913 (m-80) cc_final: 0.8684 (m-10) outliers start: 72 outliers final: 30 residues processed: 466 average time/residue: 1.3611 time to fit residues: 725.8309 Evaluate side-chains 458 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 418 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 2 ASN 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 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 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 135 MET 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 94 THR 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 428 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 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 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 214 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 287 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 231 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 L 38 GLN Z 3 ASN Z 51 GLN N 113 GLN N 201 HIS ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS G 209 ASN ** G 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.100900 restraints weight = 27673.868| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.13 r_work: 0.2587 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.461 24985 Z= 0.206 Angle : 0.768 26.062 34162 Z= 0.329 Chirality : 0.045 0.326 3592 Planarity : 0.005 0.051 4244 Dihedral : 11.048 113.997 3677 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.14 % Allowed : 19.59 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 2972 helix: 1.18 (0.13), residues: 1658 sheet: -2.37 (0.56), residues: 54 loop : 0.02 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 54 HIS 0.009 0.002 HIS I 87 PHE 0.020 0.002 PHE I 95 TYR 0.027 0.002 TYR M 240 ARG 0.009 0.001 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 1302) hydrogen bonds : angle 5.06539 ( 3741) metal coordination : bond 0.01881 ( 9) metal coordination : angle 13.16066 ( 9) SS BOND : bond 0.01791 ( 1) SS BOND : angle 4.38908 ( 2) covalent geometry : bond 0.00486 (24942) covalent geometry : angle 0.73750 (34151) Misc. bond : bond 0.18522 ( 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 520 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 445 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8494 (tp40) REVERT: J 34 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8553 (mt) REVERT: J 255 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.7206 (t80) REVERT: D 3 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6526 (mppt) REVERT: D 308 MET cc_start: 0.9005 (tpt) cc_final: 0.8765 (tpp) REVERT: M 255 TYR cc_start: 0.9135 (m-80) cc_final: 0.8826 (m-80) REVERT: N 95 TYR cc_start: 0.9170 (t80) cc_final: 0.8850 (t80) REVERT: N 105 MET cc_start: 0.9014 (mmp) cc_final: 0.8778 (mpp) REVERT: E 261 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8026 (m-70) REVERT: E 375 LYS cc_start: 0.8315 (ttpp) cc_final: 0.8052 (ptmm) REVERT: E 412 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.7981 (ttm170) REVERT: E 452 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8311 (ttp) REVERT: F 24 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7864 (mp) REVERT: F 37 ASP cc_start: 0.7812 (p0) cc_final: 0.6374 (t70) REVERT: F 184 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: G 83 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8414 (ptpp) REVERT: G 114 LYS cc_start: 0.7821 (mmmt) cc_final: 0.7588 (mtpp) REVERT: G 195 MET cc_start: 0.8363 (tpt) cc_final: 0.7804 (tpt) REVERT: G 208 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8216 (ttpp) REVERT: G 269 TYR cc_start: 0.9017 (m-80) cc_final: 0.8748 (m-10) outliers start: 75 outliers final: 36 residues processed: 483 average time/residue: 1.3696 time to fit residues: 761.6833 Evaluate side-chains 465 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 421 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 2 ASN 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 165 CYS 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 75 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 189 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 211 VAL Chi-restraints excluded: chain E residue 261 HIS 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 87 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 169 optimal weight: 0.0970 chunk 16 optimal weight: 0.0570 chunk 288 optimal weight: 3.9990 chunk 277 optimal weight: 0.0050 chunk 246 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 overall best weight: 0.3110 ------------------------------------------------------------------------------- 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** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN D 280 GLN N 201 HIS ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3669 r_free = 0.3669 target = 0.147512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.104970 restraints weight = 27905.311| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.12 r_work: 0.2668 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.422 24985 Z= 0.133 Angle : 0.782 46.703 34162 Z= 0.306 Chirality : 0.042 0.289 3592 Planarity : 0.004 0.053 4244 Dihedral : 10.474 121.826 3677 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.72 % Allowed : 20.47 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 2972 helix: 1.33 (0.13), residues: 1647 sheet: -2.33 (0.54), residues: 57 loop : -0.01 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 PHE 0.020 0.001 PHE I 255 TYR 0.025 0.002 TYR M 240 ARG 0.009 0.000 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 1302) hydrogen bonds : angle 4.94130 ( 3741) metal coordination : bond 0.03678 ( 9) metal coordination : angle 25.17839 ( 9) SS BOND : bond 0.01178 ( 1) SS BOND : angle 3.85757 ( 2) covalent geometry : bond 0.00307 (24942) covalent geometry : angle 0.66671 (34151) Misc. bond : bond 0.14983 ( 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 518 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 453 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6604 (tm-30) REVERT: C 127 LEU cc_start: 0.7120 (mt) cc_final: 0.6375 (tp) REVERT: C 166 TYR cc_start: 0.5621 (m-80) cc_final: 0.5350 (m-80) REVERT: I 150 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8389 (tp40) REVERT: I 297 TYR cc_start: 0.8965 (t80) cc_final: 0.8625 (t80) REVERT: J 34 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8525 (mt) REVERT: J 255 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6780 (t80) REVERT: K 28 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: L 34 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7672 (mmtm) REVERT: Z 102 GLN cc_start: 0.7892 (pm20) cc_final: 0.7685 (pm20) REVERT: Z 169 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7658 (mm-40) REVERT: Z 185 ASP cc_start: 0.8153 (m-30) cc_final: 0.7939 (m-30) REVERT: D 3 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6482 (mppt) REVERT: D 74 MET cc_start: 0.9106 (mmm) cc_final: 0.8868 (mmm) REVERT: D 308 MET cc_start: 0.8959 (tpt) cc_final: 0.8738 (tpp) REVERT: M 255 TYR cc_start: 0.9105 (m-80) cc_final: 0.8877 (m-80) REVERT: N 23 ASP cc_start: 0.8403 (t0) cc_final: 0.8196 (t0) REVERT: N 95 TYR cc_start: 0.9122 (t80) cc_final: 0.8838 (t80) REVERT: N 105 MET cc_start: 0.8834 (mmp) cc_final: 0.8580 (mpp) REVERT: E 261 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8003 (m-70) REVERT: E 375 LYS cc_start: 0.8255 (ttpp) cc_final: 0.8002 (ptmm) REVERT: E 412 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7914 (ttm170) REVERT: E 452 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8348 (ttp) REVERT: E 462 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6809 (pp30) REVERT: F 24 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7798 (mp) REVERT: F 37 ASP cc_start: 0.7854 (p0) cc_final: 0.6367 (t70) REVERT: F 184 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: G 8 TYR cc_start: 0.7917 (t80) cc_final: 0.7570 (t80) REVERT: G 83 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8389 (ptpp) REVERT: G 114 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7735 (mtpp) REVERT: G 208 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8260 (ttpp) outliers start: 65 outliers final: 28 residues processed: 483 average time/residue: 1.3561 time to fit residues: 749.7496 Evaluate side-chains 466 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 426 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 189 THR 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 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 169 GLN 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 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 399 SER 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 118 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 chunk 25 optimal weight: 0.0980 chunk 10 optimal weight: 0.0070 chunk 86 optimal weight: 0.7980 chunk 138 optimal weight: 0.0070 chunk 261 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 overall best weight: 0.2216 ------------------------------------------------------------------------------- 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 Z 3 ASN Z 51 GLN N 201 HIS ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3687 r_free = 0.3687 target = 0.149018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106919 restraints weight = 27920.921| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.01 r_work: 0.2714 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.394 24985 Z= 0.127 Angle : 0.766 41.333 34162 Z= 0.302 Chirality : 0.043 0.443 3592 Planarity : 0.004 0.054 4244 Dihedral : 10.182 116.138 3675 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.26 % Allowed : 20.93 % Favored : 76.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 2972 helix: 1.41 (0.13), residues: 1645 sheet: -2.28 (0.57), residues: 54 loop : 0.04 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 PHE 0.019 0.001 PHE I 255 TYR 0.028 0.002 TYR G 72 ARG 0.009 0.000 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1302) hydrogen bonds : angle 4.86410 ( 3741) metal coordination : bond 0.03289 ( 9) metal coordination : angle 24.17979 ( 9) SS BOND : bond 0.01944 ( 1) SS BOND : angle 9.44924 ( 2) covalent geometry : bond 0.00295 (24942) covalent geometry : angle 0.65352 (34151) Misc. bond : bond 0.13500 ( 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 508 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 454 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8232 (tp40) REVERT: I 297 TYR cc_start: 0.8878 (t80) cc_final: 0.8575 (t80) REVERT: J 34 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8419 (mt) REVERT: J 249 TYR cc_start: 0.8795 (t80) cc_final: 0.8506 (t80) REVERT: J 255 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.6520 (t80) REVERT: D 3 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.6541 (mppt) REVERT: D 308 MET cc_start: 0.8918 (tpt) cc_final: 0.8715 (tpp) REVERT: N 95 TYR cc_start: 0.9092 (t80) cc_final: 0.8801 (t80) REVERT: E 261 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7956 (m-70) REVERT: E 375 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7957 (ptmm) REVERT: E 412 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7870 (ttm170) REVERT: E 452 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8273 (ttp) REVERT: F 24 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7745 (mp) REVERT: F 184 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: G 195 MET cc_start: 0.7958 (tpt) cc_final: 0.7429 (tpt) REVERT: G 208 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8295 (ttpp) outliers start: 54 outliers final: 29 residues processed: 480 average time/residue: 1.3637 time to fit residues: 750.7689 Evaluate side-chains 454 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 418 time to evaluate : 2.622 ------------------------------------------------------------------------------- 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 189 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 172 GLU 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 Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 157 SER 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 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 452 MET Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 50 THR 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 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 133 optimal weight: 0.7980 chunk 260 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 259 optimal weight: 0.0970 chunk 102 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 59 optimal weight: 0.0070 chunk 285 optimal weight: 5.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 J 60 GLN K 113 GLN Z 3 ASN Z 51 GLN Z 169 GLN N 201 HIS ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 106 HIS ** 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 = 0.3677 r_free = 0.3677 target = 0.148297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105811 restraints weight = 28037.948| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.15 r_work: 0.2661 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.382 24985 Z= 0.144 Angle : 0.796 41.936 34162 Z= 0.315 Chirality : 0.043 0.312 3592 Planarity : 0.004 0.055 4244 Dihedral : 10.211 113.538 3675 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.30 % Allowed : 21.35 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 2972 helix: 1.41 (0.13), residues: 1648 sheet: -2.22 (0.57), residues: 54 loop : 0.04 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 PHE 0.018 0.001 PHE I 255 TYR 0.022 0.002 TYR G 8 ARG 0.007 0.000 ARG E 303 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 1302) hydrogen bonds : angle 4.86739 ( 3741) metal coordination : bond 0.02777 ( 9) metal coordination : angle 24.15973 ( 9) SS BOND : bond 0.00912 ( 1) SS BOND : angle 5.93182 ( 2) covalent geometry : bond 0.00339 (24942) covalent geometry : angle 0.69152 (34151) Misc. bond : bond 0.14330 ( 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 489 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 434 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6477 (tm-30) REVERT: I 150 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8298 (tp40) REVERT: I 297 TYR cc_start: 0.8954 (t80) cc_final: 0.8639 (t80) REVERT: I 313 MET cc_start: 0.9167 (ttp) cc_final: 0.8962 (ttp) REVERT: J 34 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8462 (mt) REVERT: J 249 TYR cc_start: 0.8810 (t80) cc_final: 0.8521 (t80) REVERT: J 255 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6564 (t80) REVERT: D 3 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7361 (pmtt) REVERT: D 308 MET cc_start: 0.8956 (tpt) cc_final: 0.8753 (tpp) REVERT: N 95 TYR cc_start: 0.9128 (t80) cc_final: 0.8812 (t80) REVERT: E 126 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: E 156 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8166 (ttpp) REVERT: E 261 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.8021 (m-70) REVERT: E 375 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7982 (ptmm) REVERT: E 412 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7843 (ttm170) REVERT: E 452 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8266 (ttp) REVERT: F 9 LYS cc_start: 0.6523 (mmtm) cc_final: 0.6283 (mptp) REVERT: F 24 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7800 (mp) REVERT: F 184 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: G 195 MET cc_start: 0.8045 (tpt) cc_final: 0.7307 (tpt) REVERT: G 208 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8310 (ttpp) outliers start: 55 outliers final: 28 residues processed: 461 average time/residue: 1.3697 time to fit residues: 728.5196 Evaluate side-chains 454 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 417 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 40 MET Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 181 THR 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 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 156 LYS 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 452 MET Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR 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 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 258 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 268 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 275 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 N 201 HIS ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 ASN ** G 106 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 = 0.3645 r_free = 0.3645 target = 0.145553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.102546 restraints weight = 27864.995| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.14 r_work: 0.2600 rms_B_bonded: 2.94 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: 0.8568 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.437 24985 Z= 0.192 Angle : 0.871 41.685 34162 Z= 0.349 Chirality : 0.045 0.502 3592 Planarity : 0.005 0.055 4244 Dihedral : 10.389 111.289 3675 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.93 % Allowed : 21.68 % Favored : 76.39 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 2972 helix: 1.29 (0.13), residues: 1664 sheet: -2.00 (0.60), residues: 53 loop : -0.01 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 54 HIS 0.008 0.001 HIS I 87 PHE 0.025 0.002 PHE C 133 TYR 0.025 0.002 TYR G 8 ARG 0.007 0.001 ARG J 253 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 1302) hydrogen bonds : angle 4.98051 ( 3741) metal coordination : bond 0.02853 ( 9) metal coordination : angle 24.26919 ( 9) SS BOND : bond 0.03875 ( 1) SS BOND : angle 13.00809 ( 2) covalent geometry : bond 0.00453 (24942) covalent geometry : angle 0.77063 (34151) Misc. bond : bond 0.17694 ( 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 465 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 419 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8359 (tp40) REVERT: I 297 TYR cc_start: 0.8985 (t80) cc_final: 0.8637 (t80) REVERT: I 313 MET cc_start: 0.9187 (ttp) cc_final: 0.8986 (ttp) REVERT: I 391 MET cc_start: 0.8735 (ptp) cc_final: 0.8442 (ptp) REVERT: J 34 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8415 (mt) REVERT: J 255 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6887 (t80) REVERT: K 28 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: Z 88 LEU cc_start: 0.8286 (mt) cc_final: 0.8056 (mp) REVERT: D 3 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6547 (mppt) REVERT: N 95 TYR cc_start: 0.9175 (t80) cc_final: 0.8832 (t80) REVERT: E 126 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: E 152 LYS cc_start: 0.8697 (mttm) cc_final: 0.8402 (mttt) REVERT: E 261 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.8111 (m-70) REVERT: E 375 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8106 (ptmm) REVERT: E 412 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7849 (ttm170) REVERT: E 452 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8293 (ttp) REVERT: F 9 LYS cc_start: 0.6527 (mmtm) cc_final: 0.6309 (mptp) REVERT: F 24 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7800 (mp) REVERT: F 37 ASP cc_start: 0.7841 (p0) cc_final: 0.6636 (t70) REVERT: F 137 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8378 (tpt) REVERT: F 184 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: G 195 MET cc_start: 0.8318 (tpt) cc_final: 0.7377 (tpt) REVERT: G 208 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8297 (ttpp) outliers start: 46 outliers final: 26 residues processed: 445 average time/residue: 1.3662 time to fit residues: 695.8401 Evaluate side-chains 449 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 413 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS 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 I residue 287 ILE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 40 MET 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 Z residue 181 THR 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 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 261 HIS 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 137 MET 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 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 0.0170 chunk 205 optimal weight: 0.6980 chunk 174 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 287 optimal weight: 5.9990 chunk 230 optimal weight: 0.5980 chunk 259 optimal weight: 0.0370 chunk 279 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 D 21 HIS N 201 HIS ** G 106 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 = 0.3674 r_free = 0.3674 target = 0.148056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105804 restraints weight = 28036.111| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.13 r_work: 0.2672 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.396 24985 Z= 0.140 Angle : 0.824 41.180 34162 Z= 0.330 Chirality : 0.043 0.480 3592 Planarity : 0.005 0.083 4244 Dihedral : 10.112 108.055 3675 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.67 % Allowed : 22.06 % Favored : 76.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.15), residues: 2972 helix: 1.34 (0.13), residues: 1665 sheet: -2.06 (0.61), residues: 53 loop : 0.01 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 PHE 0.018 0.001 PHE I 255 TYR 0.023 0.002 TYR G 8 ARG 0.007 0.000 ARG E 303 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 1302) hydrogen bonds : angle 4.90959 ( 3741) metal coordination : bond 0.02541 ( 9) metal coordination : angle 24.05672 ( 9) SS BOND : bond 0.03259 ( 1) SS BOND : angle 12.54654 ( 2) covalent geometry : bond 0.00332 (24942) covalent geometry : angle 0.71882 (34151) Misc. bond : bond 0.14848 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21026.13 seconds wall clock time: 361 minutes 33.62 seconds (21693.62 seconds total)