Starting phenix.real_space_refine on Sat Jun 21 07:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smr_40601/06_2025/8smr_40601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smr_40601/06_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_40601/06_2025/8smr_40601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smr_40601/06_2025/8smr_40601.map" model { file = "/net/cci-nas-00/data/ceres_data/8smr_40601/06_2025/8smr_40601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smr_40601/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.51, per 1000 atoms: 0.64 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: 7.53 Conformation dependent library (CDL) restraints added in 3.2 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: 2.39 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: 7.39 Time building geometry restraints manager: 8.51 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: 2.340 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: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 62.240 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.730 ------------------------------------------------------------------------------- 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 : 2.823 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: 1.5326 time to fit residues: 826.2774 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 : 3.130 ------------------------------------------------------------------------------- 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 = 0.104181 restraints weight = 27341.942| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.07 r_work: 0.2654 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 36.034 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 18.79146 ( 9) SS BOND : bond 0.00001 ( 1) SS BOND : angle 2.01066 ( 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 : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8613 (mt) REVERT: J 52 MET cc_start: 0.9002 (mtp) cc_final: 0.8793 (mtm) REVERT: K 28 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: Z 75 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8755 (m) REVERT: Z 76 HIS cc_start: 0.8513 (t-90) cc_final: 0.8193 (t-90) REVERT: Z 164 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8264 (mtm180) REVERT: D 3 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6562 (mppt) REVERT: D 308 MET cc_start: 0.8864 (tpt) cc_final: 0.8618 (tpp) REVERT: N 95 TYR cc_start: 0.9143 (t80) cc_final: 0.8864 (t80) REVERT: E 229 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8473 (mmmt) REVERT: E 239 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7511 (mmm-85) REVERT: E 252 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.5979 (m-10) REVERT: E 410 MET cc_start: 0.8459 (mmm) cc_final: 0.8251 (mtm) REVERT: E 469 LEU cc_start: 0.8180 (mt) cc_final: 0.7978 (pp) REVERT: F 24 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7476 (mp) REVERT: F 127 ASN cc_start: 0.8772 (t0) cc_final: 0.8502 (t0) REVERT: F 151 LYS cc_start: 0.6582 (mmmt) cc_final: 0.6321 (mmtt) REVERT: F 182 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7704 (ptpt) REVERT: F 184 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: F 197 THR cc_start: 0.9007 (m) cc_final: 0.8802 (m) REVERT: G 45 ASP cc_start: 0.7963 (t70) cc_final: 0.7004 (t0) REVERT: G 195 MET cc_start: 0.8375 (tpt) cc_final: 0.7957 (tpt) REVERT: G 256 MET cc_start: 0.8265 (mtm) cc_final: 0.8027 (mtt) outliers start: 66 outliers final: 18 residues processed: 481 average time/residue: 1.4491 time to fit residues: 800.8224 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 : 2.528 ------------------------------------------------------------------------------- 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: 2.9990 chunk 209 optimal weight: 0.9980 chunk 287 optimal weight: 20.0000 chunk 184 optimal weight: 0.0030 chunk 110 optimal weight: 7.9990 chunk 182 optimal weight: 0.0470 chunk 291 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 280 GLN J 177 GLN Z 3 ASN Z 51 GLN D 361 GLN ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106127 restraints weight = 27655.815| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.10 r_work: 0.2679 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.424 24985 Z= 0.137 Angle : 0.713 30.675 34162 Z= 0.299 Chirality : 0.042 0.257 3592 Planarity : 0.005 0.053 4244 Dihedral : 11.638 127.991 3677 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.14 % Allowed : 18.46 % Favored : 78.40 % 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: 0.99 (0.15), residues: 2972 helix: 1.29 (0.13), residues: 1646 sheet: -2.20 (0.60), residues: 54 loop : 0.06 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 147 HIS 0.007 0.001 HIS E 300 PHE 0.023 0.001 PHE I 255 TYR 0.021 0.002 TYR D 388 ARG 0.007 0.000 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 1302) hydrogen bonds : angle 5.13004 ( 3741) metal coordination : bond 0.01751 ( 9) metal coordination : angle 15.94503 ( 9) SS BOND : bond 0.00093 ( 1) SS BOND : angle 2.28143 ( 2) covalent geometry : bond 0.00314 (24942) covalent geometry : angle 0.66397 (34151) Misc. bond : bond 0.15501 ( 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 536 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 461 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8467 (tp40) REVERT: J 34 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8600 (mt) REVERT: K 23 ASP cc_start: 0.8326 (t0) cc_final: 0.8044 (t70) REVERT: K 28 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: K 101 MET cc_start: 0.9126 (ttm) cc_final: 0.8825 (ttm) REVERT: Z 76 HIS cc_start: 0.8520 (t-90) cc_final: 0.8146 (t-90) REVERT: Z 147 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7936 (mtpp) REVERT: D 3 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6580 (mppt) REVERT: D 308 MET cc_start: 0.8913 (tpt) cc_final: 0.8658 (tpp) REVERT: N 95 TYR cc_start: 0.9123 (t80) cc_final: 0.8804 (t80) REVERT: E 229 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8422 (mmmt) REVERT: E 252 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.6099 (m-10) REVERT: E 412 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7900 (ttm170) REVERT: E 462 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7227 (pt0) REVERT: F 24 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7558 (mp) REVERT: F 151 LYS cc_start: 0.6568 (mmmt) cc_final: 0.6140 (mmtt) REVERT: F 184 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: G 45 ASP cc_start: 0.8158 (t70) cc_final: 0.7163 (t0) REVERT: G 83 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8181 (ptpp) REVERT: G 195 MET cc_start: 0.8273 (tpt) cc_final: 0.7813 (tpt) REVERT: G 269 TYR cc_start: 0.8756 (m-80) cc_final: 0.8520 (m-10) outliers start: 75 outliers final: 23 residues processed: 494 average time/residue: 1.3870 time to fit residues: 784.8871 Evaluate side-chains 464 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 432 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 147 LYS 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 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 252 TYR 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 184 GLU 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: 2.9990 chunk 241 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 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 = 0.3649 r_free = 0.3649 target = 0.145975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.102464 restraints weight = 27913.459| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.14 r_work: 0.2614 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.443 24985 Z= 0.191 Angle : 0.761 28.924 34162 Z= 0.321 Chirality : 0.045 0.278 3592 Planarity : 0.005 0.051 4244 Dihedral : 11.590 125.463 3677 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.60 % Allowed : 18.88 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.15), residues: 2972 helix: 1.19 (0.13), residues: 1652 sheet: -2.25 (0.59), residues: 54 loop : 0.04 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 54 HIS 0.009 0.002 HIS I 87 PHE 0.021 0.002 PHE I 95 TYR 0.024 0.002 TYR M 240 ARG 0.007 0.001 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 1302) hydrogen bonds : angle 5.11658 ( 3741) metal coordination : bond 0.01962 ( 9) metal coordination : angle 14.64533 ( 9) SS BOND : bond 0.00886 ( 1) SS BOND : angle 5.16836 ( 2) covalent geometry : bond 0.00446 (24942) covalent geometry : angle 0.72177 (34151) Misc. bond : bond 0.17856 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 443 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ASP cc_start: 0.5745 (m-30) cc_final: 0.5468 (m-30) REVERT: I 150 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8463 (tp40) REVERT: J 34 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8645 (mt) REVERT: J 255 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.7083 (t80) REVERT: K 101 MET cc_start: 0.9180 (ttm) cc_final: 0.8902 (ttm) REVERT: Z 75 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8877 (m) REVERT: Z 76 HIS cc_start: 0.8592 (t-90) cc_final: 0.8249 (t-90) REVERT: Z 114 LYS cc_start: 0.8212 (mttt) cc_final: 0.7952 (ptpt) REVERT: Z 147 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7988 (mtpp) REVERT: Z 164 ARG cc_start: 0.8642 (mtm180) cc_final: 0.8322 (mtm180) REVERT: D 3 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6549 (mppt) REVERT: D 308 MET cc_start: 0.8961 (tpt) cc_final: 0.8705 (tpp) REVERT: N 95 TYR cc_start: 0.9161 (t80) cc_final: 0.8817 (t80) REVERT: E 261 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7791 (m-70) REVERT: E 412 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.7989 (ttm170) REVERT: E 452 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8260 (ttp) REVERT: F 24 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7144 (mp) REVERT: F 151 LYS cc_start: 0.6520 (mmmt) cc_final: 0.6158 (mmtt) REVERT: F 184 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: G 45 ASP cc_start: 0.8311 (t70) cc_final: 0.7412 (t0) REVERT: G 73 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8081 (tp) REVERT: G 83 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8362 (ptpp) REVERT: G 195 MET cc_start: 0.8349 (tpt) cc_final: 0.7787 (tpt) REVERT: G 269 TYR cc_start: 0.8917 (m-80) cc_final: 0.8658 (m-10) outliers start: 86 outliers final: 35 residues processed: 483 average time/residue: 1.4821 time to fit residues: 821.5702 Evaluate side-chains 461 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 415 time to evaluate : 2.895 ------------------------------------------------------------------------------- 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 K residue 82 THR Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 147 LYS Chi-restraints excluded: chain Z residue 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 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 73 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 1.9990 chunk 163 optimal weight: 0.0570 chunk 118 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 189 optimal weight: 0.6980 chunk 247 optimal weight: 0.1980 chunk 235 optimal weight: 3.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN L 38 GLN Z 3 ASN Z 51 GLN N 113 GLN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.104844 restraints weight = 27907.549| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.13 r_work: 0.2643 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.406 24985 Z= 0.141 Angle : 0.701 26.356 34162 Z= 0.299 Chirality : 0.042 0.256 3592 Planarity : 0.004 0.048 4244 Dihedral : 11.176 120.202 3677 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.10 % Allowed : 19.80 % Favored : 77.10 % 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: 0.97 (0.15), residues: 2972 helix: 1.30 (0.13), residues: 1642 sheet: -2.21 (0.59), residues: 56 loop : 0.03 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 147 HIS 0.013 0.001 HIS C 76 PHE 0.021 0.001 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 0.04352 ( 1302) hydrogen bonds : angle 5.00937 ( 3741) metal coordination : bond 0.01573 ( 9) metal coordination : angle 13.50480 ( 9) SS BOND : bond 0.00371 ( 1) SS BOND : angle 3.14922 ( 2) covalent geometry : bond 0.00330 (24942) covalent geometry : angle 0.66561 (34151) Misc. bond : bond 0.15025 ( 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 514 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 440 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6611 (tm-30) REVERT: I 150 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8391 (tp40) REVERT: J 34 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8587 (mt) REVERT: J 132 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8697 (mt-10) REVERT: J 189 GLU cc_start: 0.7394 (tp30) cc_final: 0.6968 (tp30) REVERT: J 255 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6788 (t80) REVERT: K 28 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: Z 76 HIS cc_start: 0.8525 (t-90) cc_final: 0.8173 (t-90) REVERT: Z 114 LYS cc_start: 0.8189 (mttt) cc_final: 0.7895 (ptpt) REVERT: D 3 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6512 (mppt) REVERT: D 74 MET cc_start: 0.9080 (mmm) cc_final: 0.8877 (mmm) REVERT: D 280 GLN cc_start: 0.8628 (mt0) cc_final: 0.8411 (mt0) REVERT: D 308 MET cc_start: 0.8957 (tpt) cc_final: 0.8711 (tpp) REVERT: N 95 TYR cc_start: 0.9135 (t80) cc_final: 0.8842 (t80) REVERT: E 261 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7867 (m-70) REVERT: E 412 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.8017 (ttm170) REVERT: E 452 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8259 (ttp) REVERT: E 462 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6946 (pp30) REVERT: F 24 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7728 (mp) REVERT: F 37 ASP cc_start: 0.7705 (p0) cc_final: 0.6208 (t70) REVERT: F 151 LYS cc_start: 0.6543 (mmmt) cc_final: 0.6268 (mmtt) REVERT: F 184 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: G 31 GLN cc_start: 0.8426 (mt0) cc_final: 0.8199 (mp10) REVERT: G 40 VAL cc_start: 0.4038 (t) cc_final: 0.3789 (m) REVERT: G 45 ASP cc_start: 0.8348 (t70) cc_final: 0.7607 (t0) REVERT: G 73 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8173 (tp) REVERT: G 83 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8395 (ptpp) REVERT: G 195 MET cc_start: 0.8232 (tpt) cc_final: 0.7625 (tpt) REVERT: G 269 TYR cc_start: 0.8914 (m-80) cc_final: 0.8672 (m-10) outliers start: 74 outliers final: 26 residues processed: 474 average time/residue: 1.3701 time to fit residues: 746.4770 Evaluate side-chains 462 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 425 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 167 SER 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 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 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: 6.9990 chunk 23 optimal weight: 0.6980 chunk 287 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 282 optimal weight: 9.9990 chunk 236 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 L 38 GLN Z 3 ASN Z 51 GLN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 ASN ** G 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.101704 restraints weight = 27715.676| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.13 r_work: 0.2616 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.447 24985 Z= 0.190 Angle : 0.754 26.072 34162 Z= 0.322 Chirality : 0.045 0.303 3592 Planarity : 0.005 0.052 4244 Dihedral : 10.943 113.943 3677 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.06 % Allowed : 19.59 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.15), residues: 2972 helix: 1.20 (0.13), residues: 1658 sheet: -2.27 (0.57), residues: 54 loop : 0.03 (0.17), residues: 1260 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 0.019 0.002 PHE I 95 TYR 0.025 0.002 TYR C 105 ARG 0.009 0.001 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 1302) hydrogen bonds : angle 5.06619 ( 3741) metal coordination : bond 0.01758 ( 9) metal coordination : angle 13.29891 ( 9) SS BOND : bond 0.01710 ( 1) SS BOND : angle 3.52995 ( 2) covalent geometry : bond 0.00449 (24942) covalent geometry : angle 0.72167 (34151) Misc. bond : bond 0.17877 ( 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 517 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 444 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8479 (tp40) REVERT: J 34 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8610 (mt) REVERT: J 255 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.7183 (t80) REVERT: Z 164 ARG cc_start: 0.8601 (mtm180) cc_final: 0.8286 (mtm180) REVERT: D 3 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6526 (mppt) REVERT: D 308 MET cc_start: 0.9017 (tpt) cc_final: 0.8778 (tpp) REVERT: N 95 TYR cc_start: 0.9169 (t80) cc_final: 0.8802 (t80) REVERT: N 105 MET cc_start: 0.8924 (mmp) cc_final: 0.8514 (mpp) REVERT: E 261 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.8028 (m-70) REVERT: E 375 LYS cc_start: 0.8303 (ttpp) cc_final: 0.8041 (ptmm) REVERT: E 412 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7943 (ttm170) REVERT: E 452 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8321 (ttp) REVERT: F 24 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7834 (mp) REVERT: F 37 ASP cc_start: 0.7799 (p0) cc_final: 0.6355 (t70) REVERT: F 151 LYS cc_start: 0.6575 (mmmt) cc_final: 0.6255 (mmtt) REVERT: F 184 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: G 31 GLN cc_start: 0.8641 (mt0) cc_final: 0.8388 (mt0) REVERT: G 40 VAL cc_start: 0.4516 (t) cc_final: 0.4310 (m) REVERT: G 83 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8391 (ptpp) REVERT: G 114 LYS cc_start: 0.7845 (mmmt) cc_final: 0.7609 (mtpp) REVERT: G 195 MET cc_start: 0.8339 (tpt) cc_final: 0.7786 (tpt) REVERT: G 208 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8219 (ttpp) REVERT: G 269 TYR cc_start: 0.8996 (m-80) cc_final: 0.8749 (m-10) outliers start: 73 outliers final: 38 residues processed: 479 average time/residue: 1.4739 time to fit residues: 814.3182 Evaluate side-chains 474 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 428 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 ASP 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 165 CYS Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 390 ARG 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 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 F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 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: 0.7980 chunk 16 optimal weight: 0.3980 chunk 288 optimal weight: 5.9990 chunk 277 optimal weight: 0.0970 chunk 246 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN D 280 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104938 restraints weight = 27885.698| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.19 r_work: 0.2649 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.421 24985 Z= 0.145 Angle : 0.786 44.505 34162 Z= 0.309 Chirality : 0.043 0.286 3592 Planarity : 0.004 0.051 4244 Dihedral : 10.542 121.213 3677 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.89 % Allowed : 20.09 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.13), residues: 1660 sheet: -2.26 (0.55), residues: 57 loop : -0.00 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 147 HIS 0.007 0.001 HIS G 294 PHE 0.019 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 0.04355 ( 1302) hydrogen bonds : angle 4.98981 ( 3741) metal coordination : bond 0.04081 ( 9) metal coordination : angle 24.82223 ( 9) SS BOND : bond 0.00285 ( 1) SS BOND : angle 5.28441 ( 2) covalent geometry : bond 0.00336 (24942) covalent geometry : angle 0.67434 (34151) Misc. bond : bond 0.15924 ( 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: 69 poor density : 449 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 TYR cc_start: 0.5707 (m-80) cc_final: 0.5504 (m-80) REVERT: I 150 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8429 (tp40) REVERT: I 297 TYR cc_start: 0.8982 (t80) cc_final: 0.8680 (t80) REVERT: J 34 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8452 (mt) REVERT: J 255 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6859 (t80) REVERT: K 28 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: L 34 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7752 (mmtm) REVERT: Z 164 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8286 (mtm180) REVERT: Z 169 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7758 (mm-40) REVERT: D 3 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6517 (mppt) REVERT: D 308 MET cc_start: 0.8985 (tpt) cc_final: 0.8764 (tpp) REVERT: N 23 ASP cc_start: 0.8423 (t0) cc_final: 0.8221 (t0) REVERT: N 95 TYR cc_start: 0.9134 (t80) cc_final: 0.8824 (t80) REVERT: E 126 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: E 261 HIS cc_start: 0.8499 (OUTLIER) cc_final: 0.8059 (m-70) REVERT: E 375 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8025 (ptmm) REVERT: E 412 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7929 (ttm170) REVERT: E 452 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8329 (ttp) REVERT: E 462 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6836 (pp30) REVERT: F 24 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7804 (mp) REVERT: F 37 ASP cc_start: 0.7841 (p0) cc_final: 0.6380 (t70) REVERT: F 151 LYS cc_start: 0.6555 (mmmt) cc_final: 0.6283 (mmtt) REVERT: F 184 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: G 8 TYR cc_start: 0.7913 (t80) cc_final: 0.7608 (t80) REVERT: G 31 GLN cc_start: 0.8653 (mt0) cc_final: 0.8424 (mt0) REVERT: G 83 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8401 (ptpp) REVERT: G 114 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7761 (mtpp) REVERT: G 195 MET cc_start: 0.8255 (tpt) cc_final: 0.7620 (tpt) REVERT: G 208 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8321 (ttpp) outliers start: 69 outliers final: 35 residues processed: 480 average time/residue: 1.4124 time to fit residues: 777.9658 Evaluate side-chains 469 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 421 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain 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 252 TYR Chi-restraints excluded: chain E residue 261 HIS 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 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 118 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 137 optimal weight: 0.0970 chunk 25 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 138 optimal weight: 0.0570 chunk 261 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 overall best weight: 0.2096 ------------------------------------------------------------------------------- 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 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 = 0.3682 r_free = 0.3682 target = 0.148675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107768 restraints weight = 27891.722| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.18 r_work: 0.2702 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.404 24985 Z= 0.128 Angle : 0.776 43.472 34162 Z= 0.305 Chirality : 0.043 0.479 3592 Planarity : 0.004 0.053 4244 Dihedral : 10.198 116.951 3675 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.55 % Allowed : 20.76 % Favored : 76.68 % 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: 1.03 (0.15), residues: 2972 helix: 1.36 (0.13), residues: 1647 sheet: -2.28 (0.55), residues: 57 loop : 0.04 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 PHE 0.023 0.001 PHE C 151 TYR 0.025 0.002 TYR M 240 ARG 0.009 0.000 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 1302) hydrogen bonds : angle 4.90588 ( 3741) metal coordination : bond 0.03347 ( 9) metal coordination : angle 24.34628 ( 9) SS BOND : bond 0.02148 ( 1) SS BOND : angle 9.10428 ( 2) covalent geometry : bond 0.00296 (24942) covalent geometry : angle 0.66471 (34151) Misc. bond : bond 0.14054 ( 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 512 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 451 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6482 (tm-30) REVERT: C 166 TYR cc_start: 0.5650 (m-80) cc_final: 0.5371 (m-80) REVERT: I 150 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8357 (tp40) REVERT: I 297 TYR cc_start: 0.8940 (t80) cc_final: 0.8618 (t80) REVERT: J 34 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8205 (mt) REVERT: J 60 GLN cc_start: 0.8752 (tt0) cc_final: 0.8544 (tt0) REVERT: J 132 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8625 (mt-10) REVERT: J 249 TYR cc_start: 0.8797 (t80) cc_final: 0.8506 (t80) REVERT: J 255 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6489 (t80) REVERT: D 3 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6573 (mppt) REVERT: M 255 TYR cc_start: 0.9100 (m-80) cc_final: 0.8893 (m-80) REVERT: N 95 TYR cc_start: 0.9108 (t80) cc_final: 0.8795 (t80) REVERT: E 126 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: E 261 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.8000 (m-70) REVERT: E 375 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7966 (ptmm) REVERT: E 412 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7852 (ttm170) REVERT: E 452 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8271 (ttp) REVERT: E 462 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6732 (pp30) REVERT: F 24 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7851 (mp) REVERT: F 184 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: G 8 TYR cc_start: 0.7947 (t80) cc_final: 0.7650 (t80) REVERT: G 31 GLN cc_start: 0.8674 (mt0) cc_final: 0.8461 (mt0) REVERT: G 208 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8261 (ttpp) outliers start: 61 outliers final: 30 residues processed: 484 average time/residue: 1.8492 time to fit residues: 1029.3787 Evaluate side-chains 481 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 442 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER 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 191 CYS 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 157 SER 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 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 126 GLU 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 E residue 462 GLN 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 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 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 Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 133 optimal weight: 0.6980 chunk 260 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 285 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN Z 169 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 = 0.3657 r_free = 0.3657 target = 0.146641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.104262 restraints weight = 27900.072| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.13 r_work: 0.2654 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.430 24985 Z= 0.158 Angle : 0.808 42.945 34162 Z= 0.319 Chirality : 0.044 0.435 3592 Planarity : 0.004 0.054 4244 Dihedral : 10.297 113.333 3675 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.39 % Allowed : 21.26 % Favored : 76.35 % 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: 1.01 (0.15), residues: 2972 helix: 1.35 (0.13), residues: 1646 sheet: -2.11 (0.56), residues: 56 loop : 0.01 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.007 0.001 HIS E 258 PHE 0.017 0.001 PHE I 255 TYR 0.030 0.002 TYR G 72 ARG 0.007 0.000 ARG E 303 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 1302) hydrogen bonds : angle 4.94221 ( 3741) metal coordination : bond 0.02841 ( 9) metal coordination : angle 24.29194 ( 9) SS BOND : bond 0.03188 ( 1) SS BOND : angle 8.58912 ( 2) covalent geometry : bond 0.00372 (24942) covalent geometry : angle 0.70247 (34151) Misc. bond : bond 0.15578 ( 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 511 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 454 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 166 TYR cc_start: 0.5665 (m-80) cc_final: 0.5392 (m-80) REVERT: I 150 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8411 (tp40) REVERT: I 297 TYR cc_start: 0.8967 (t80) cc_final: 0.8676 (t80) REVERT: J 34 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8174 (mt) REVERT: J 255 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.6725 (t80) REVERT: K 28 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: K 100 LYS cc_start: 0.8619 (tptt) cc_final: 0.8418 (tptp) REVERT: D 3 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6546 (mppt) REVERT: D 308 MET cc_start: 0.8730 (tpp) cc_final: 0.8403 (tpt) REVERT: M 255 TYR cc_start: 0.9141 (m-80) cc_final: 0.8911 (m-80) REVERT: N 95 TYR cc_start: 0.9147 (t80) cc_final: 0.8857 (t80) REVERT: E 126 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: E 261 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.8048 (m-70) REVERT: E 412 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7847 (ttm170) REVERT: E 452 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8298 (ttp) REVERT: E 462 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6765 (pp30) REVERT: F 24 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7875 (mp) REVERT: F 184 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: G 195 MET cc_start: 0.8243 (tpt) cc_final: 0.7451 (tpt) REVERT: G 208 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8315 (ttpp) outliers start: 57 outliers final: 33 residues processed: 484 average time/residue: 1.4299 time to fit residues: 798.2002 Evaluate side-chains 474 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 431 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 191 CYS 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 157 SER Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 258 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 275 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.146252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.103397 restraints weight = 27816.253| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.15 r_work: 0.2626 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2494 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= 0.168 Angle : 0.858 41.406 34162 Z= 0.345 Chirality : 0.045 0.517 3592 Planarity : 0.005 0.054 4244 Dihedral : 10.319 110.479 3675 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.22 % Allowed : 21.77 % Favored : 76.02 % 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: 1.27 (0.13), residues: 1663 sheet: -2.10 (0.56), residues: 56 loop : 0.03 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.007 0.001 HIS I 87 PHE 0.020 0.002 PHE E 91 TYR 0.028 0.002 TYR M 240 ARG 0.010 0.000 ARG C 10 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 1302) hydrogen bonds : angle 4.99789 ( 3741) metal coordination : bond 0.02664 ( 9) metal coordination : angle 24.21586 ( 9) SS BOND : bond 0.04367 ( 1) SS BOND : angle 11.39139 ( 2) covalent geometry : bond 0.00392 (24942) covalent geometry : angle 0.75750 (34151) Misc. bond : bond 0.16786 ( 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 488 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 435 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6509 (tm-30) REVERT: C 166 TYR cc_start: 0.5685 (m-80) cc_final: 0.5391 (m-80) REVERT: I 150 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8490 (tp40) REVERT: I 190 ILE cc_start: 0.9009 (mt) cc_final: 0.8792 (mp) REVERT: I 297 TYR cc_start: 0.8974 (t80) cc_final: 0.8739 (t80) REVERT: J 34 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8093 (mt) REVERT: J 255 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6811 (t80) REVERT: K 28 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: K 100 LYS cc_start: 0.8620 (tptt) cc_final: 0.8408 (tptp) REVERT: D 3 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.6521 (mppt) REVERT: D 308 MET cc_start: 0.8734 (tpp) cc_final: 0.8441 (tpt) REVERT: N 95 TYR cc_start: 0.9170 (t80) cc_final: 0.8853 (t80) REVERT: E 126 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: E 152 LYS cc_start: 0.8704 (mttm) cc_final: 0.8411 (mttt) REVERT: E 261 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.8005 (m-70) REVERT: E 412 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7856 (ttm170) REVERT: E 452 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8283 (ttp) REVERT: E 462 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6791 (pp30) REVERT: F 24 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7809 (mp) REVERT: F 137 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8569 (tpt) REVERT: F 170 GLU cc_start: 0.8033 (mp0) cc_final: 0.7699 (mp0) REVERT: F 184 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: G 195 MET cc_start: 0.8298 (tpt) cc_final: 0.7446 (tpt) REVERT: G 208 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8298 (ttpp) outliers start: 53 outliers final: 33 residues processed: 463 average time/residue: 1.4108 time to fit residues: 747.3387 Evaluate side-chains 464 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 420 time to evaluate : 2.780 ------------------------------------------------------------------------------- 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 191 CYS 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 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 180 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 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 E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 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 Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 278 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 0.1980 chunk 205 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 287 optimal weight: 0.0370 chunk 230 optimal weight: 0.5980 chunk 259 optimal weight: 0.6980 chunk 279 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 176 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 = 0.3672 r_free = 0.3672 target = 0.147778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.105172 restraints weight = 27975.296| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.07 r_work: 0.2675 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2643 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= 0.142 Angle : 0.832 41.405 34162 Z= 0.333 Chirality : 0.044 0.513 3592 Planarity : 0.004 0.054 4244 Dihedral : 10.144 106.860 3675 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.09 % Allowed : 21.81 % Favored : 76.10 % 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: 0.99 (0.15), residues: 2972 helix: 1.29 (0.13), residues: 1668 sheet: -2.02 (0.59), residues: 56 loop : 0.04 (0.17), residues: 1248 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 0.020 0.001 PHE J 243 TYR 0.025 0.002 TYR M 240 ARG 0.013 0.000 ARG C 134 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 1302) hydrogen bonds : angle 4.95625 ( 3741) metal coordination : bond 0.02548 ( 9) metal coordination : angle 24.10158 ( 9) SS BOND : bond 0.04350 ( 1) SS BOND : angle 11.54357 ( 2) covalent geometry : bond 0.00331 (24942) covalent geometry : angle 0.72866 (34151) Misc. bond : bond 0.15190 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23201.02 seconds wall clock time: 403 minutes 52.28 seconds (24232.28 seconds total)