Starting phenix.real_space_refine on Sun Jul 5 00:56:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8smr_40601/07_2026/8smr_40601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smr_40601/07_2026/8smr_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_40601/07_2026/8smr_40601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smr_40601/07_2026/8smr_40601.map" model { file = "/net/cci-nas-00/data/ceres_data/8smr_40601/07_2026/8smr_40601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smr_40601/07_2026/8smr_40601.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8smr_40601/07_2026/8smr_40601.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8smr_40601/07_2026/8smr_40601.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.182 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 19 7.16 5 Cu 1 5.60 5 S 141 5.16 5 C 15890 2.51 5 N 3934 2.21 5 O 4167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24154 Number of models: 1 Model: "" Number of chains: 24 Chain: "C" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1420 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 20, 'TRANS': 169} Chain: "I" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3267 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "J" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1842 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 13, 'TRANS': 218} Chain: "K" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1306 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "L" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 115 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "Z" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1449 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 20, 'TRANS': 173} Chain: "D" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3267 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "M" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1631 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "N" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1306 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "O" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 115 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 452} Chain: "F" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1499 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 188} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "G" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2345 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 16, 'TRANS': 295} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'HEM': 2, 'I7Y': 1, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 11 Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'FES': 1, 'I7Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'HEM': 2, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 89 Unusual residues: {' CA': 2, ' CU': 1, 'HEM': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 878 SG CYS C 124 85.827 89.782 77.166 1.00 85.05 S ATOM 913 SG CYS C 129 82.197 90.933 76.398 1.00 88.42 S ATOM 1090 SG CYS C 152 83.421 92.466 78.335 1.00 90.53 S ATOM 8848 SG CYS Z 124 43.111 59.333 39.809 1.00 50.08 S ATOM 9060 SG CYS Z 152 46.380 59.925 38.108 1.00 53.09 S Time building chain proxies: 4.53, per 1000 atoms: 0.19 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: 1.99 Conformation dependent library (CDL) restraints added in 939.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 155 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 126 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 152 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 124 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 129 " pdb=" FES Z 201 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 155 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 126 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 152 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 124 " Number of angles added : 9 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5452 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 19 sheets defined 61.7% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'C' and resid 7 through 36 Proline residue: C 32 - end of helix Processing helix chain 'C' and resid 40 through 47 Processing helix chain 'C' and resid 78 through 85 removed outlier: 3.528A pdb=" N LEU C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 4.364A pdb=" N GLU C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 92 " --> pdb=" O GLU C 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 12 removed outlier: 3.587A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 Processing helix chain 'I' and resid 32 through 35 Processing helix chain 'I' and resid 36 through 57 Processing helix chain 'I' and resid 65 through 76 Processing helix chain 'I' and resid 79 through 108 Processing helix chain 'I' and resid 115 through 139 removed outlier: 3.520A pdb=" N LEU I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU I 139 " --> pdb=" O MET I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 156 removed outlier: 3.992A pdb=" N PHE I 156 " --> pdb=" O ILE I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'I' and resid 162 through 172 Processing helix chain 'I' and resid 177 through 190 Processing helix chain 'I' and resid 190 through 211 Processing helix chain 'I' and resid 219 through 223 Processing helix chain 'I' and resid 236 through 262 removed outlier: 6.667A pdb=" N THR I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 276 Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 293 through 303 Processing helix chain 'I' and resid 305 through 327 removed outlier: 3.663A pdb=" N ILE I 317 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU I 320 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 322 " --> pdb=" O ALA I 318 " (cutoff:3.500A) Proline residue: I 324 - end of helix Processing helix chain 'I' and resid 333 through 337 Processing helix chain 'I' and resid 338 through 360 Processing helix chain 'I' and resid 364 through 384 removed outlier: 3.918A pdb=" N PHE I 382 " --> pdb=" O TYR I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 392 removed outlier: 4.255A pdb=" N ARG I 390 " --> pdb=" O PRO I 386 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I 392 " --> pdb=" O TYR I 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 51 Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 72 through 80 Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 119 through 128 removed outlier: 3.546A pdb=" N ARG J 128 " --> pdb=" O TYR J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 159 Processing helix chain 'J' and resid 204 through 224 Processing helix chain 'J' and resid 226 through 254 Processing helix chain 'K' and resid 23 through 31 removed outlier: 3.956A pdb=" N ALA K 29 " --> pdb=" O ALA K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 56 through 69 Processing helix chain 'K' and resid 74 through 78 Processing helix chain 'K' and resid 85 through 98 Processing helix chain 'K' and resid 107 through 121 removed outlier: 4.569A pdb=" N ALA K 112 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN K 113 " --> pdb=" O ASN K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 Processing helix chain 'K' and resid 176 through 184 removed outlier: 3.878A pdb=" N LYS K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 199 removed outlier: 3.547A pdb=" N GLY K 199 " --> pdb=" O SER K 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'Z' and resid 9 through 36 Proline residue: Z 32 - end of helix Processing helix chain 'Z' and resid 42 through 46 removed outlier: 3.532A pdb=" N ALA Z 45 " --> pdb=" O LYS Z 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA Z 46 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 46' Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 86 through 92 removed outlier: 4.822A pdb=" N GLY Z 90 " --> pdb=" O SER Z 87 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Z 92 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.598A pdb=" N ARG D 11 " --> pdb=" O TRP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 32 through 35 Processing helix chain 'D' and resid 36 through 57 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 79 through 109 Processing helix chain 'D' and resid 115 through 139 removed outlier: 3.576A pdb=" N LEU D 139 " --> pdb=" O MET D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 156 removed outlier: 4.063A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'D' and resid 190 through 211 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 236 through 262 removed outlier: 6.719A pdb=" N THR D 241 " --> pdb=" O HIS D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 303 removed outlier: 3.596A pdb=" N VAL D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 322 removed outlier: 4.103A pdb=" N LEU D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 338 through 359 Processing helix chain 'D' and resid 364 through 384 removed outlier: 3.879A pdb=" N PHE D 382 " --> pdb=" O TYR D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 392 removed outlier: 4.342A pdb=" N ARG D 390 " --> pdb=" O PRO D 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 51 Processing helix chain 'M' and resid 62 through 70 Processing helix chain 'M' and resid 72 through 80 Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 113 through 118 Processing helix chain 'M' and resid 119 through 128 removed outlier: 3.541A pdb=" N ARG M 128 " --> pdb=" O TYR M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 159 Processing helix chain 'M' and resid 204 through 224 Processing helix chain 'M' and resid 226 through 256 removed outlier: 3.610A pdb=" N TYR M 236 " --> pdb=" O ARG M 232 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE M 247 " --> pdb=" O PHE M 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 31 removed outlier: 3.866A pdb=" N ALA N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 Processing helix chain 'N' and resid 56 through 69 Processing helix chain 'N' and resid 74 through 78 Processing helix chain 'N' and resid 85 through 98 Processing helix chain 'N' and resid 107 through 121 removed outlier: 4.662A pdb=" N ALA N 112 " --> pdb=" O PRO N 108 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLN N 113 " --> pdb=" O ASN N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 166 Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'N' and resid 186 through 199 Processing helix chain 'O' and resid 25 through 29 Processing helix chain 'E' and resid 11 through 42 removed outlier: 4.040A pdb=" N VAL E 15 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 49 through 52 Processing helix chain 'E' and resid 53 through 68 Proline residue: E 59 - end of helix removed outlier: 3.778A pdb=" N ILE E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 87 removed outlier: 4.165A pdb=" N GLN E 83 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 114 Processing helix chain 'E' and resid 133 through 152 Processing helix chain 'E' and resid 159 through 180 removed outlier: 5.108A pdb=" N HIS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 211 removed outlier: 4.083A pdb=" N ASN E 209 " --> pdb=" O TRP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 232 Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 237 through 253 removed outlier: 4.409A pdb=" N ILE E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 261 removed outlier: 3.617A pdb=" N HIS E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS E 261 " --> pdb=" O HIS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 294 removed outlier: 4.386A pdb=" N ALA E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Proline residue: E 283 - end of helix Processing helix chain 'E' and resid 298 through 304 Processing helix chain 'E' and resid 305 through 329 Proline residue: E 326 - end of helix Processing helix chain 'E' and resid 330 through 337 removed outlier: 3.919A pdb=" N LEU E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 352 removed outlier: 4.222A pdb=" N ILE E 344 " --> pdb=" O THR E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 371 Proline residue: E 368 - end of helix Processing helix chain 'E' and resid 378 through 413 removed outlier: 3.861A pdb=" N GLY E 392 " --> pdb=" O LEU E 388 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU E 395 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 396 " --> pdb=" O GLY E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 461 Proline residue: E 433 - end of helix Processing helix chain 'E' and resid 464 through 473 removed outlier: 3.871A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 4.292A pdb=" N LEU F 7 " --> pdb=" O ASN F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 30 removed outlier: 4.066A pdb=" N GLY F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR F 28 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F 29 " --> pdb=" O GLY F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 64 through 68 removed outlier: 3.686A pdb=" N GLY F 67 " --> pdb=" O GLY F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.797A pdb=" N VAL F 93 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 127 through 132 removed outlier: 4.148A pdb=" N VAL F 131 " --> pdb=" O ASN F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 163 Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.555A pdb=" N ARG F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'G' and resid 2 through 28 Processing helix chain 'G' and resid 55 through 76 Processing helix chain 'G' and resid 103 through 127 Proline residue: G 121 - end of helix Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 137 through 152 Processing helix chain 'G' and resid 152 through 157 Processing helix chain 'G' and resid 179 through 190 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 230 through 241 removed outlier: 3.571A pdb=" N THR G 240 " --> pdb=" O GLN G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 283 Processing helix chain 'G' and resid 291 through 312 removed outlier: 3.847A pdb=" N LEU G 295 " --> pdb=" O GLN G 291 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASN G 297 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N ASP G 298 " --> pdb=" O HIS G 294 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 50 through 53 removed outlier: 6.810A pdb=" N THR C 189 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE C 182 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 67 Processing sheet with id=AA3, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AA4, first strand: chain 'I' and resid 26 through 28 Processing sheet with id=AA5, first strand: chain 'J' and resid 57 through 61 removed outlier: 3.780A pdb=" N MET J 91 " --> pdb=" O ALA J 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 130 through 132 Processing sheet with id=AA7, first strand: chain 'J' and resid 161 through 169 removed outlier: 6.185A pdb=" N VAL J 162 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU J 194 " --> pdb=" O VAL J 162 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY J 164 " --> pdb=" O ASP J 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'K' and resid 200 through 201 Processing sheet with id=AB1, first strand: chain 'Z' and resid 50 through 53 removed outlier: 6.695A pdb=" N THR Z 189 " --> pdb=" O PHE Z 182 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N PHE Z 182 " --> pdb=" O THR Z 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 61 through 67 removed outlier: 3.856A pdb=" N GLN Z 61 " --> pdb=" O HIS Z 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 132 through 134 Processing sheet with id=AB4, first strand: chain 'D' and resid 26 through 28 Processing sheet with id=AB5, first strand: chain 'M' and resid 57 through 61 removed outlier: 3.889A pdb=" N MET M 91 " --> pdb=" O ALA M 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 130 through 132 Processing sheet with id=AB7, first strand: chain 'M' and resid 161 through 162 Processing sheet with id=AB8, first strand: chain 'N' and resid 200 through 201 Processing sheet with id=AB9, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.828A pdb=" N LYS E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 191 through 192 1302 hydrogen bonds defined for protein. 3741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.36: 7519 1.36 - 1.57: 17094 1.57 - 1.78: 29 1.78 - 1.99: 232 1.99 - 2.21: 68 Bond restraints: 24942 Sorted by residual: bond pdb=" C07 I7Y Z 202 " pdb=" C08 I7Y Z 202 " ideal model delta sigma weight residual 1.542 1.253 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C07 I7Y I 504 " pdb=" C08 I7Y I 504 " ideal model delta sigma weight residual 1.542 1.253 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C07 I7Y I 504 " pdb=" C15 I7Y I 504 " ideal model delta sigma weight residual 1.526 1.775 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C07 I7Y Z 202 " pdb=" C15 I7Y Z 202 " ideal model delta sigma weight residual 1.526 1.775 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C02 I7Y I 504 " pdb=" C10 I7Y I 504 " ideal model delta sigma weight residual 1.526 1.295 0.231 2.00e-02 2.50e+03 1.33e+02 ... (remaining 24937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 34104 6.76 - 13.53: 40 13.53 - 20.29: 3 20.29 - 27.05: 0 27.05 - 33.82: 4 Bond angle restraints: 34151 Sorted by residual: angle pdb=" C74 I7Y I 504 " pdb=" C73 I7Y I 504 " pdb=" C76 I7Y I 504 " ideal model delta sigma weight residual 114.35 148.17 -33.82 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C74 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C76 I7Y Z 202 " ideal model delta sigma weight residual 114.35 148.16 -33.81 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C74 I7Y I 504 " pdb=" C73 I7Y I 504 " pdb=" O80 I7Y I 504 " ideal model delta sigma weight residual 107.63 79.89 27.74 3.00e+00 1.11e-01 8.55e+01 angle pdb=" C74 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" O80 I7Y Z 202 " ideal model delta sigma weight residual 107.63 79.90 27.73 3.00e+00 1.11e-01 8.54e+01 angle pdb=" CB GLN Z 169 " pdb=" CG GLN Z 169 " pdb=" CD GLN Z 169 " ideal model delta sigma weight residual 112.60 98.34 14.26 1.70e+00 3.46e-01 7.04e+01 ... (remaining 34146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 13154 24.23 - 48.47: 925 48.47 - 72.70: 168 72.70 - 96.94: 67 96.94 - 121.17: 15 Dihedral angle restraints: 14329 sinusoidal: 5768 harmonic: 8561 Sorted by residual: dihedral pdb=" C2B HEC J 500 " pdb=" C3B HEC J 500 " pdb=" CAB HEC J 500 " pdb=" CBB HEC J 500 " ideal model delta sinusoidal sigma weight residual 60.00 132.70 -72.70 2 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" C2C HEC N 501 " pdb=" C3C HEC N 501 " pdb=" CAC HEC N 501 " pdb=" CBC HEC N 501 " ideal model delta sinusoidal sigma weight residual 60.00 116.70 -56.70 2 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" C6 U10 D 503 " pdb=" C7 U10 D 503 " pdb=" C8 U10 D 503 " pdb=" C9 U10 D 503 " ideal model delta sinusoidal sigma weight residual 101.51 -147.21 -111.27 1 2.00e+01 2.50e-03 3.27e+01 ... (remaining 14326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 3583 0.282 - 0.565: 5 0.565 - 0.847: 2 0.847 - 1.130: 0 1.130 - 1.412: 2 Chirality restraints: 3592 Sorted by residual: chirality pdb=" C74 I7Y I 504 " pdb=" C03 I7Y I 504 " pdb=" C73 I7Y I 504 " pdb=" C75 I7Y I 504 " both_signs ideal model delta sigma weight residual False -2.55 -1.14 -1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" C74 I7Y Z 202 " pdb=" C03 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C75 I7Y Z 202 " both_signs ideal model delta sigma weight residual False -2.55 -1.14 -1.41 2.00e-01 2.50e+01 4.98e+01 chirality pdb=" C02 I7Y I 504 " pdb=" C03 I7Y I 504 " pdb=" C06 I7Y I 504 " pdb=" C10 I7Y I 504 " both_signs ideal model delta sigma weight residual False 2.93 2.25 0.68 2.00e-01 2.50e+01 1.14e+01 ... (remaining 3589 not shown) Planarity restraints: 4244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC N 501 " -0.025 2.00e-02 2.50e+03 6.32e-02 8.99e+01 pdb=" C2C HEC N 501 " 0.173 2.00e-02 2.50e+03 pdb=" C3C HEC N 501 " -0.016 2.00e-02 2.50e+03 pdb=" C4C HEC N 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC N 501 " -0.040 2.00e-02 2.50e+03 pdb=" CHC HEC N 501 " -0.031 2.00e-02 2.50e+03 pdb=" CHD HEC N 501 " 0.006 2.00e-02 2.50e+03 pdb=" CMC HEC N 501 " -0.048 2.00e-02 2.50e+03 pdb=" NC HEC N 501 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 501 " -0.018 2.00e-02 2.50e+03 5.68e-02 7.26e+01 pdb=" C2C HEC K 501 " 0.155 2.00e-02 2.50e+03 pdb=" C3C HEC K 501 " -0.037 2.00e-02 2.50e+03 pdb=" C4C HEC K 501 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC K 501 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEC K 501 " -0.027 2.00e-02 2.50e+03 pdb=" CHD HEC K 501 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC K 501 " -0.046 2.00e-02 2.50e+03 pdb=" NC HEC K 501 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC G 401 " -0.010 2.00e-02 2.50e+03 5.11e-02 5.87e+01 pdb=" C2C HEC G 401 " 0.137 2.00e-02 2.50e+03 pdb=" C3C HEC G 401 " -0.045 2.00e-02 2.50e+03 pdb=" C4C HEC G 401 " -0.006 2.00e-02 2.50e+03 pdb=" CAC HEC G 401 " -0.011 2.00e-02 2.50e+03 pdb=" CHC HEC G 401 " -0.025 2.00e-02 2.50e+03 pdb=" CHD HEC G 401 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC G 401 " -0.042 2.00e-02 2.50e+03 pdb=" NC HEC G 401 " -0.001 2.00e-02 2.50e+03 ... (remaining 4241 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 253 2.56 - 3.14: 20082 3.14 - 3.73: 42450 3.73 - 4.31: 59958 4.31 - 4.90: 97746 Nonbonded interactions: 220489 Sorted by model distance: nonbonded pdb=" OG SER F 135 " pdb=" O1D HEC F 301 " model vdw 1.975 3.040 nonbonded pdb=" OG SER N 85 " pdb=" OD1 ASP N 88 " model vdw 2.024 3.040 nonbonded pdb=" OG1 THR C 181 " pdb=" OE1 GLN C 194 " model vdw 2.054 3.040 nonbonded pdb=" O LEU N 75 " pdb=" OG1 THR N 78 " model vdw 2.096 3.040 nonbonded pdb=" OH TYR E 238 " pdb=" OE2 GLU F 8 " model vdw 2.097 3.040 ... (remaining 220484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 6 through 195) selection = (chain 'Z' and resid 6 through 195) } ncs_group { reference = chain 'D' selection = (chain 'I' and resid 1 through 503) } ncs_group { reference = (chain 'J' and (resid 26 through 163 or resid 193 through 500)) selection = (chain 'M' and resid 26 through 500) } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.120 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.377 24985 Z= 0.421 Angle : 0.902 35.633 34162 Z= 0.392 Chirality : 0.058 1.412 3592 Planarity : 0.005 0.063 4244 Dihedral : 18.183 121.174 8874 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 0.92 % Allowed : 19.42 % Favored : 79.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 2972 helix: 1.10 (0.13), residues: 1628 sheet: -2.47 (0.63), residues: 46 loop : -0.01 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 253 TYR 0.014 0.001 TYR I 388 PHE 0.024 0.001 PHE I 255 TRP 0.015 0.001 TRP I 54 HIS 0.013 0.001 HIS Z 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.38 (24942) covalent geometry : angle 0.84181 / 0.39 (34151) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 0.27200 / 0.16 ( 2) hydrogen bonds : bond 0.13827 / 9.27 ( 1302) hydrogen bonds : angle 6.54112 / 4.69 ( 3741) metal coordination : bond 0.01173 / 0.55 ( 9) metal coordination : angle 20.06080 / 10.02 ( 9) Misc. bond : bond 0.15247 / 10.95 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 456 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 52 MET cc_start: 0.8975 (mtp) cc_final: 0.8678 (mtm) REVERT: K 23 ASP cc_start: 0.7961 (t0) cc_final: 0.7717 (t70) REVERT: Z 76 HIS cc_start: 0.8477 (t-90) cc_final: 0.8212 (t-90) REVERT: D 3 LYS cc_start: 0.7442 (mptt) cc_final: 0.6407 (mppt) REVERT: E 229 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8578 (mmmt) REVERT: E 261 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7421 (t-90) REVERT: E 410 MET cc_start: 0.8123 (mmm) cc_final: 0.7703 (mtm) REVERT: F 24 ILE cc_start: 0.7745 (mm) cc_final: 0.7469 (mp) REVERT: F 197 THR cc_start: 0.8972 (m) cc_final: 0.8746 (m) REVERT: G 45 ASP cc_start: 0.7812 (t70) cc_final: 0.7326 (t70) REVERT: G 195 MET cc_start: 0.8324 (tpt) cc_final: 0.7882 (tpt) outliers start: 22 outliers final: 15 residues processed: 469 average time/residue: 0.6019 time to fit residues: 325.6548 Evaluate side-chains 426 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 410 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 361 GLN Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 473 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 192 HIS Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.3655 r_free = 0.3655 target = 0.146637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.102744 restraints weight = 27364.904| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.06 r_work: 0.2626 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.419 24985 Z= 0.186 Angle : 0.798 36.013 34162 Z= 0.333 Chirality : 0.045 0.249 3592 Planarity : 0.005 0.052 4244 Dihedral : 12.309 128.767 3696 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 18.08 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.15), residues: 2972 helix: 1.10 (0.13), residues: 1659 sheet: -2.33 (0.68), residues: 42 loop : 0.07 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 10 TYR 0.022 0.002 TYR C 105 PHE 0.027 0.002 PHE I 255 TRP 0.017 0.001 TRP D 147 HIS 0.008 0.001 HIS E 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (24942) covalent geometry : angle 0.73639 / 0.33 (34151) SS BOND : bond 0.00984 / 0.52 ( 1) SS BOND : angle 2.22004 / 1.31 ( 2) hydrogen bonds : bond 0.05081 / 3.46 ( 1302) hydrogen bonds : angle 5.38652 / 3.88 ( 3741) metal coordination : bond 0.02351 / 1.18 ( 9) metal coordination : angle 18.95536 / 9.38 ( 9) Misc. bond : bond 0.17900 / 12.73 ( 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 515 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 448 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8642 (mt) REVERT: J 52 MET cc_start: 0.9058 (mtp) cc_final: 0.8792 (mtm) REVERT: K 28 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: L 34 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7730 (mmtm) REVERT: Z 75 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8751 (m) REVERT: Z 76 HIS cc_start: 0.8524 (t-90) cc_final: 0.8188 (t-90) REVERT: Z 164 ARG cc_start: 0.8598 (mtm180) cc_final: 0.8254 (mtm180) REVERT: D 3 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.6564 (mppt) REVERT: D 308 MET cc_start: 0.8874 (tpt) cc_final: 0.8631 (tpp) REVERT: N 95 TYR cc_start: 0.9133 (t80) cc_final: 0.8835 (t80) REVERT: E 229 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8485 (mmmt) REVERT: E 239 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7548 (mmm-85) REVERT: E 410 MET cc_start: 0.8495 (mmm) cc_final: 0.8238 (mtm) REVERT: E 469 LEU cc_start: 0.8194 (mt) cc_final: 0.7976 (pp) REVERT: F 24 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7479 (mp) REVERT: F 127 ASN cc_start: 0.8781 (t0) cc_final: 0.8498 (t0) REVERT: F 147 LYS cc_start: 0.8003 (pttm) cc_final: 0.7790 (mtmt) REVERT: F 151 LYS cc_start: 0.6563 (mmmt) cc_final: 0.6290 (mmtt) REVERT: F 184 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: F 197 THR cc_start: 0.9033 (m) cc_final: 0.8826 (m) REVERT: G 45 ASP cc_start: 0.7978 (t70) cc_final: 0.7040 (t0) REVERT: G 195 MET cc_start: 0.8411 (tpt) cc_final: 0.8037 (tpt) outliers start: 67 outliers final: 20 residues processed: 480 average time/residue: 0.6249 time to fit residues: 345.6687 Evaluate side-chains 451 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 423 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 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 217 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 199 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 9 optimal weight: 0.0030 chunk 248 optimal weight: 6.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 150 GLN I 280 GLN J 177 GLN Z 3 ASN Z 51 GLN D 361 GLN E 203 GLN E 209 ASN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS G 31 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.102864 restraints weight = 27433.450| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.18 r_work: 0.2606 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.418 24985 Z= 0.171 Angle : 0.750 31.940 34162 Z= 0.315 Chirality : 0.044 0.254 3592 Planarity : 0.005 0.050 4244 Dihedral : 11.849 127.619 3677 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.52 % Allowed : 18.21 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.15), residues: 2972 helix: 1.14 (0.13), residues: 1660 sheet: -2.20 (0.59), residues: 54 loop : 0.04 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 10 TYR 0.019 0.002 TYR D 388 PHE 0.023 0.002 PHE I 255 TRP 0.018 0.001 TRP D 147 HIS 0.007 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (24942) covalent geometry : angle 0.69961 / 0.31 (34151) SS BOND : bond 0.00479 / 0.25 ( 1) SS BOND : angle 2.26772 / 1.33 ( 2) hydrogen bonds : bond 0.04802 / 3.28 ( 1302) hydrogen bonds : angle 5.20570 / 3.75 ( 3741) metal coordination : bond 0.01932 / 1.04 ( 9) metal coordination : angle 16.68153 / 8.29 ( 9) Misc. bond : bond 0.17487 / 12.49 ( 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 530 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 446 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8629 (mt) REVERT: J 255 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6937 (t80) REVERT: K 28 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: Z 75 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8806 (m) REVERT: Z 76 HIS cc_start: 0.8565 (t-90) cc_final: 0.8210 (t-90) REVERT: Z 147 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.7947 (mtpp) REVERT: D 3 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6600 (mppt) REVERT: D 305 ASP cc_start: 0.8688 (t0) cc_final: 0.8486 (t0) REVERT: D 308 MET cc_start: 0.8960 (tpt) cc_final: 0.8715 (tpp) REVERT: N 95 TYR cc_start: 0.9157 (t80) cc_final: 0.8848 (t80) REVERT: E 412 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7966 (ttm170) REVERT: E 462 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7195 (pt0) REVERT: F 24 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7648 (mp) REVERT: F 127 ASN cc_start: 0.8820 (t0) cc_final: 0.8577 (t0) REVERT: F 151 LYS cc_start: 0.6658 (mmmt) cc_final: 0.6440 (mmtt) REVERT: F 184 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: G 45 ASP cc_start: 0.8255 (t70) cc_final: 0.7365 (t0) REVERT: G 83 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8351 (ptpp) REVERT: G 195 MET cc_start: 0.8336 (tpt) cc_final: 0.7860 (tpt) REVERT: G 256 MET cc_start: 0.8355 (mtm) cc_final: 0.8139 (mtt) REVERT: G 269 TYR cc_start: 0.8865 (m-80) cc_final: 0.8556 (m-10) outliers start: 84 outliers final: 29 residues processed: 485 average time/residue: 0.6049 time to fit residues: 337.3596 Evaluate side-chains 461 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 422 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 147 LYS Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 LEU 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 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 192 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 150 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 244 optimal weight: 0.0980 chunk 149 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 243 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 203 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103545 restraints weight = 27796.922| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.16 r_work: 0.2655 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.416 24985 Z= 0.147 Angle : 0.715 28.642 34162 Z= 0.301 Chirality : 0.043 0.271 3592 Planarity : 0.005 0.050 4244 Dihedral : 11.482 125.884 3677 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.39 % Allowed : 18.96 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.15), residues: 2972 helix: 1.22 (0.13), residues: 1654 sheet: -2.30 (0.60), residues: 54 loop : 0.03 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 10 TYR 0.024 0.002 TYR M 240 PHE 0.022 0.001 PHE I 255 TRP 0.027 0.001 TRP C 146 HIS 0.008 0.001 HIS E 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (24942) covalent geometry : angle 0.67338 / 0.30 (34151) SS BOND : bond 0.00555 / 0.29 ( 1) SS BOND : angle 1.87592 / 1.06 ( 2) hydrogen bonds : bond 0.04466 / 3.05 ( 1302) hydrogen bonds : angle 5.06416 / 3.65 ( 3741) metal coordination : bond 0.01643 / 0.76 ( 9) metal coordination : angle 14.82071 / 7.41 ( 9) Misc. bond : bond 0.16414 / 11.76 ( 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 519 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 438 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8635 (mt) REVERT: J 255 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6766 (t80) REVERT: K 28 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: K 101 MET cc_start: 0.9164 (ttm) cc_final: 0.8826 (ttm) REVERT: Z 75 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8843 (m) REVERT: Z 76 HIS cc_start: 0.8525 (t-90) cc_final: 0.8123 (t-90) REVERT: D 3 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.6537 (mppt) REVERT: D 308 MET cc_start: 0.8999 (tpt) cc_final: 0.8776 (tpp) REVERT: M 255 TYR cc_start: 0.9143 (m-80) cc_final: 0.8931 (m-80) REVERT: N 28 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: N 95 TYR cc_start: 0.9145 (t80) cc_final: 0.8811 (t80) REVERT: E 261 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7839 (m-70) REVERT: E 412 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7988 (ttm170) REVERT: E 452 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8272 (ttp) REVERT: F 24 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7614 (mp) REVERT: F 127 ASN cc_start: 0.8768 (t0) cc_final: 0.8522 (t0) REVERT: F 151 LYS cc_start: 0.6563 (mmmt) cc_final: 0.6202 (mmtt) REVERT: F 184 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: G 45 ASP cc_start: 0.8264 (t70) cc_final: 0.7483 (t0) REVERT: G 83 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8352 (ptpp) REVERT: G 195 MET cc_start: 0.8272 (tpt) cc_final: 0.7751 (tpt) REVERT: G 256 MET cc_start: 0.8342 (mtm) cc_final: 0.8141 (mtt) REVERT: G 269 TYR cc_start: 0.8879 (m-80) cc_final: 0.8632 (m-10) outliers start: 81 outliers final: 30 residues processed: 474 average time/residue: 0.6204 time to fit residues: 337.6653 Evaluate side-chains 461 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 420 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 28 GLN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 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 G residue 50 TYR Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 192 HIS Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 288 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 134 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 0.0070 chunk 196 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 253 optimal weight: 0.4980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN J 90 HIS K 113 GLN L 38 GLN Z 3 ASN Z 51 GLN N 201 HIS E 203 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.148125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105774 restraints weight = 27704.158| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.11 r_work: 0.2659 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.417 24985 Z= 0.134 Angle : 0.691 26.310 34162 Z= 0.293 Chirality : 0.042 0.292 3592 Planarity : 0.004 0.051 4244 Dihedral : 11.132 120.049 3677 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.52 % Allowed : 19.17 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 2972 helix: 1.35 (0.13), residues: 1642 sheet: -2.32 (0.58), residues: 57 loop : 0.05 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 10 TYR 0.024 0.002 TYR M 240 PHE 0.021 0.001 PHE I 255 TRP 0.015 0.001 TRP D 147 HIS 0.008 0.001 HIS C 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (24942) covalent geometry : angle 0.65484 / 0.29 (34151) SS BOND : bond 0.00490 / 0.26 ( 1) SS BOND : angle 2.37425 / 1.40 ( 2) hydrogen bonds : bond 0.04272 / 2.92 ( 1302) hydrogen bonds : angle 4.98703 / 3.59 ( 3741) metal coordination : bond 0.01504 / 0.65 ( 9) metal coordination : angle 13.54831 / 6.80 ( 9) Misc. bond : bond 0.15158 / 10.76 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 435 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 297 TYR cc_start: 0.8994 (t80) cc_final: 0.8634 (t80) REVERT: J 34 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8616 (mt) REVERT: J 255 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6711 (t80) REVERT: Z 76 HIS cc_start: 0.8525 (t-90) cc_final: 0.8134 (t-90) REVERT: Z 161 LEU cc_start: 0.9110 (mt) cc_final: 0.8908 (mt) REVERT: D 3 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.6533 (mppt) REVERT: D 308 MET cc_start: 0.8951 (tpt) cc_final: 0.8702 (tpp) REVERT: N 95 TYR cc_start: 0.9114 (t80) cc_final: 0.8796 (t80) REVERT: E 156 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8126 (ttpp) REVERT: E 261 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.7871 (m-70) REVERT: E 412 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.8017 (ttm170) REVERT: E 452 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8233 (ttp) REVERT: E 462 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6899 (pp30) REVERT: F 9 LYS cc_start: 0.6734 (mmtp) cc_final: 0.6387 (mmtm) REVERT: F 24 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7243 (mp) REVERT: F 108 ASP cc_start: 0.8147 (t70) cc_final: 0.7865 (t70) REVERT: F 127 ASN cc_start: 0.8774 (t0) cc_final: 0.8521 (t0) REVERT: F 151 LYS cc_start: 0.6576 (mmmt) cc_final: 0.6332 (mmtt) REVERT: F 184 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: G 40 VAL cc_start: 0.4099 (t) cc_final: 0.3830 (m) REVERT: G 83 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8371 (ptpp) REVERT: G 195 MET cc_start: 0.8175 (tpt) cc_final: 0.7581 (tpt) REVERT: G 269 TYR cc_start: 0.8893 (m-80) cc_final: 0.8653 (m-10) outliers start: 84 outliers final: 33 residues processed: 476 average time/residue: 0.6060 time to fit residues: 331.6967 Evaluate side-chains 464 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 421 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 192 HIS Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 288 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 118 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 8 optimal weight: 9.9990 chunk 178 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 113 GLN N 201 HIS E 203 GLN ** 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 = 0.3673 r_free = 0.3673 target = 0.147802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.105253 restraints weight = 27864.619| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.12 r_work: 0.2658 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.396 24985 Z= 0.136 Angle : 0.696 25.242 34162 Z= 0.296 Chirality : 0.042 0.313 3592 Planarity : 0.004 0.052 4244 Dihedral : 10.629 113.473 3677 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.14 % Allowed : 19.97 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.15), residues: 2972 helix: 1.40 (0.13), residues: 1640 sheet: -2.26 (0.58), residues: 57 loop : 0.06 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 10 TYR 0.025 0.002 TYR M 240 PHE 0.019 0.001 PHE I 255 TRP 0.015 0.001 TRP D 147 HIS 0.008 0.001 HIS C 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (24942) covalent geometry : angle 0.66392 / 0.29 (34151) SS BOND : bond 0.01284 / 0.68 ( 1) SS BOND : angle 2.40048 / 1.30 ( 2) hydrogen bonds : bond 0.04228 / 2.89 ( 1302) hydrogen bonds : angle 4.94146 / 3.55 ( 3741) metal coordination : bond 0.01364 / 0.60 ( 9) metal coordination : angle 12.91017 / 6.52 ( 9) Misc. bond : bond 0.14700 / 10.46 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 435 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6562 (tm-30) REVERT: C 127 LEU cc_start: 0.7068 (mt) cc_final: 0.6375 (tp) REVERT: I 287 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8034 (mt) REVERT: I 297 TYR cc_start: 0.8944 (t80) cc_final: 0.8653 (t80) REVERT: J 34 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8537 (mt) REVERT: J 255 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.6585 (t80) REVERT: K 28 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: Z 76 HIS cc_start: 0.8494 (t-90) cc_final: 0.8093 (t-90) REVERT: D 3 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6522 (mppt) REVERT: D 308 MET cc_start: 0.8953 (tpt) cc_final: 0.8716 (tpp) REVERT: N 28 GLN cc_start: 0.8882 (tt0) cc_final: 0.8625 (tt0) REVERT: N 95 TYR cc_start: 0.9116 (t80) cc_final: 0.8805 (t80) REVERT: E 156 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8109 (ttpp) REVERT: E 181 MET cc_start: 0.7426 (tpp) cc_final: 0.7206 (mmm) REVERT: E 261 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7906 (m-70) REVERT: E 412 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7914 (ttm170) REVERT: E 452 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8213 (ttp) REVERT: E 462 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6930 (pp30) REVERT: F 9 LYS cc_start: 0.6662 (mmtp) cc_final: 0.6286 (mmtm) REVERT: F 24 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7802 (mp) REVERT: F 37 ASP cc_start: 0.7742 (p0) cc_final: 0.6322 (t70) REVERT: F 108 ASP cc_start: 0.8149 (t70) cc_final: 0.7937 (t70) REVERT: F 151 LYS cc_start: 0.6586 (mmmt) cc_final: 0.6342 (mmtt) REVERT: F 184 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: G 40 VAL cc_start: 0.4243 (t) cc_final: 0.4037 (m) REVERT: G 83 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8370 (ptpp) REVERT: G 208 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8272 (ttpp) REVERT: G 269 TYR cc_start: 0.8908 (m-80) cc_final: 0.8683 (m-10) outliers start: 75 outliers final: 38 residues processed: 472 average time/residue: 0.6380 time to fit residues: 346.0251 Evaluate side-chains 471 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 421 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 I residue 287 ILE Chi-restraints excluded: chain I residue 361 GLN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 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 188 MET 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 193 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN Z 3 ASN Z 51 GLN N 201 HIS E 203 GLN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.103099 restraints weight = 27830.423| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.11 r_work: 0.2609 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.433 24985 Z= 0.174 Angle : 0.803 44.455 34162 Z= 0.313 Chirality : 0.044 0.309 3592 Planarity : 0.004 0.055 4244 Dihedral : 10.500 120.631 3675 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.93 % Allowed : 20.18 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.15), residues: 2972 helix: 1.28 (0.13), residues: 1657 sheet: -2.37 (0.53), residues: 57 loop : 0.02 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 10 TYR 0.025 0.002 TYR M 240 PHE 0.018 0.002 PHE I 95 TRP 0.017 0.001 TRP I 54 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (24942) covalent geometry : angle 0.69427 / 0.31 (34151) SS BOND : bond 0.01152 / 0.61 ( 1) SS BOND : angle 2.53036 / 1.36 ( 2) hydrogen bonds : bond 0.04543 / 3.12 ( 1302) hydrogen bonds : angle 4.99601 / 3.61 ( 3741) metal coordination : bond 0.03649 / 1.69 ( 9) metal coordination : angle 24.78981 / 12.90 ( 9) Misc. bond : bond 0.16651 / 11.90 ( 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 512 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 442 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 287 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8283 (mt) REVERT: I 297 TYR cc_start: 0.8985 (t80) cc_final: 0.8724 (t80) REVERT: J 34 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8534 (mt) REVERT: J 255 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6978 (t80) REVERT: Z 169 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7783 (mm-40) REVERT: D 3 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6526 (mppt) REVERT: D 308 MET cc_start: 0.9002 (tpt) cc_final: 0.8771 (tpp) REVERT: N 95 TYR cc_start: 0.9155 (t80) cc_final: 0.8830 (t80) REVERT: E 126 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: E 261 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8004 (m-70) REVERT: E 375 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8019 (ptmm) REVERT: E 412 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7947 (ttm170) REVERT: E 452 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8274 (ttp) REVERT: E 462 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6884 (pp30) REVERT: F 24 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7716 (mp) REVERT: F 37 ASP cc_start: 0.7830 (p0) cc_final: 0.6405 (t70) REVERT: F 151 LYS cc_start: 0.6568 (mmmt) cc_final: 0.6259 (mmtt) REVERT: F 184 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: G 83 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8409 (ptpp) REVERT: G 114 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7722 (mtpp) REVERT: G 195 MET cc_start: 0.8218 (tpt) cc_final: 0.7558 (tpt) REVERT: G 208 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8342 (ttpp) REVERT: G 269 TYR cc_start: 0.8963 (m-80) cc_final: 0.8756 (m-10) outliers start: 70 outliers final: 44 residues processed: 480 average time/residue: 0.6756 time to fit residues: 372.8608 Evaluate side-chains 477 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 421 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain 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 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 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 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 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 87 SER Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 145 optimal weight: 0.2980 chunk 218 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 53 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN Z 3 ASN Z 51 GLN D 280 GLN N 201 HIS E 203 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.146136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103548 restraints weight = 27748.630| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.11 r_work: 0.2614 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.423 24985 Z= 0.165 Angle : 0.802 42.304 34162 Z= 0.314 Chirality : 0.043 0.330 3592 Planarity : 0.005 0.067 4244 Dihedral : 10.409 117.525 3675 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.80 % Allowed : 20.51 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.15), residues: 2972 helix: 1.25 (0.13), residues: 1659 sheet: -2.30 (0.54), residues: 57 loop : 0.02 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 10 TYR 0.030 0.002 TYR G 72 PHE 0.022 0.002 PHE C 151 TRP 0.016 0.001 TRP I 54 HIS 0.007 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (24942) covalent geometry : angle 0.69659 / 0.31 (34151) SS BOND : bond 0.00043 / 0.02 ( 1) SS BOND : angle 2.43685 / 1.30 ( 2) hydrogen bonds : bond 0.04482 / 3.08 ( 1302) hydrogen bonds : angle 4.98238 / 3.60 ( 3741) metal coordination : bond 0.03287 / 1.47 ( 9) metal coordination : angle 24.48967 / 12.72 ( 9) Misc. bond : bond 0.16501 / 11.75 ( 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 500 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 433 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6675 (tm-30) REVERT: C 94 ASP cc_start: 0.5524 (m-30) cc_final: 0.5166 (m-30) REVERT: I 297 TYR cc_start: 0.8969 (t80) cc_final: 0.8672 (t80) REVERT: J 34 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8426 (mt) REVERT: J 255 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.7019 (t80) REVERT: Z 102 GLN cc_start: 0.7926 (pm20) cc_final: 0.7701 (pm20) REVERT: D 3 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.6526 (mppt) REVERT: D 308 MET cc_start: 0.8978 (tpt) cc_final: 0.8774 (tpp) REVERT: N 95 TYR cc_start: 0.9150 (t80) cc_final: 0.8819 (t80) REVERT: E 126 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: E 261 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8077 (m-70) REVERT: E 375 LYS cc_start: 0.8272 (ttpp) cc_final: 0.8065 (ptmm) REVERT: E 412 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7920 (ttm170) REVERT: E 452 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8247 (ttp) REVERT: E 462 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6873 (pp30) REVERT: F 9 LYS cc_start: 0.6599 (mmtp) cc_final: 0.6378 (mmtm) REVERT: F 24 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7796 (mp) REVERT: F 151 LYS cc_start: 0.6543 (mmmt) cc_final: 0.6266 (mmtt) REVERT: F 184 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: G 106 HIS cc_start: 0.7832 (m-70) cc_final: 0.7623 (m-70) REVERT: G 114 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7802 (mtpp) REVERT: G 195 MET cc_start: 0.8246 (tpt) cc_final: 0.7456 (tpt) REVERT: G 208 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8314 (ttpp) REVERT: G 269 TYR cc_start: 0.8957 (m-80) cc_final: 0.8749 (m-10) outliers start: 67 outliers final: 39 residues processed: 465 average time/residue: 0.6957 time to fit residues: 371.1298 Evaluate side-chains 472 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 424 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 40 MET 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 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 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 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 87 SER Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 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 219 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 257 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 237 optimal weight: 0.9980 chunk 286 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 53 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN Z 3 ASN Z 51 GLN N 201 HIS ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103352 restraints weight = 27712.054| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.09 r_work: 0.2628 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.404 24985 Z= 0.154 Angle : 0.792 42.506 34162 Z= 0.311 Chirality : 0.043 0.344 3592 Planarity : 0.005 0.058 4244 Dihedral : 10.328 113.183 3675 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.60 % Allowed : 20.80 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.15), residues: 2972 helix: 1.28 (0.13), residues: 1659 sheet: -2.26 (0.54), residues: 57 loop : 0.00 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 10 TYR 0.030 0.002 TYR G 72 PHE 0.017 0.001 PHE I 255 TRP 0.016 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (24942) covalent geometry : angle 0.68642 / 0.31 (34151) SS BOND : bond 0.00442 / 0.23 ( 1) SS BOND : angle 2.49682 / 1.32 ( 2) hydrogen bonds : bond 0.04415 / 3.03 ( 1302) hydrogen bonds : angle 4.95504 / 3.58 ( 3741) metal coordination : bond 0.02708 / 1.21 ( 9) metal coordination : angle 24.33327 / 12.61 ( 9) Misc. bond : bond 0.16181 / 11.48 ( 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 497 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 435 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 297 TYR cc_start: 0.8956 (t80) cc_final: 0.8614 (t80) REVERT: J 34 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8178 (mt) REVERT: J 255 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6978 (t80) REVERT: Z 102 GLN cc_start: 0.7893 (pm20) cc_final: 0.7683 (pm20) REVERT: D 3 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6502 (mppt) REVERT: D 308 MET cc_start: 0.8984 (tpt) cc_final: 0.8779 (tpp) REVERT: N 95 TYR cc_start: 0.9144 (t80) cc_final: 0.8827 (t80) REVERT: E 126 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: E 261 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.8095 (m-70) REVERT: E 375 LYS cc_start: 0.8292 (ttpp) cc_final: 0.8064 (ptmm) REVERT: E 412 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7834 (ttm170) REVERT: E 452 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8229 (ttp) REVERT: E 462 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6813 (pp30) REVERT: F 9 LYS cc_start: 0.6583 (mmtp) cc_final: 0.6366 (mmtm) REVERT: F 24 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7781 (mp) REVERT: F 184 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: G 106 HIS cc_start: 0.7897 (m-70) cc_final: 0.7690 (m-70) REVERT: G 195 MET cc_start: 0.8208 (tpt) cc_final: 0.7442 (tpt) REVERT: G 208 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8313 (ttpp) REVERT: G 269 TYR cc_start: 0.8961 (m-80) cc_final: 0.8761 (m-10) outliers start: 62 outliers final: 37 residues processed: 467 average time/residue: 0.6224 time to fit residues: 334.3499 Evaluate side-chains 470 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 424 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU 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 J residue 34 LEU Chi-restraints excluded: chain J residue 40 MET 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 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 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 126 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 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 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 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 33 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 249 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 53 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN Z 3 ASN Z 51 GLN N 201 HIS E 203 GLN ** 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 = 0.3652 r_free = 0.3652 target = 0.146257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.103444 restraints weight = 27793.773| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.14 r_work: 0.2613 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.415 24985 Z= 0.160 Angle : 0.810 41.072 34162 Z= 0.320 Chirality : 0.043 0.338 3592 Planarity : 0.005 0.059 4244 Dihedral : 10.301 109.821 3675 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.18 % Allowed : 21.35 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.15), residues: 2972 helix: 1.28 (0.13), residues: 1654 sheet: -2.19 (0.54), residues: 57 loop : -0.01 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 10 TYR 0.028 0.002 TYR M 240 PHE 0.020 0.002 PHE E 91 TRP 0.016 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 (24942) covalent geometry : angle 0.70871 / 0.32 (34151) SS BOND : bond 0.00219 / 0.12 ( 1) SS BOND : angle 2.52039 / 1.33 ( 2) hydrogen bonds : bond 0.04481 / 3.08 ( 1302) hydrogen bonds : angle 4.96839 / 3.58 ( 3741) metal coordination : bond 0.02655 / 1.18 ( 9) metal coordination : angle 24.20617 / 12.52 ( 9) Misc. bond : bond 0.16769 / 11.86 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 427 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6663 (tm-30) REVERT: I 297 TYR cc_start: 0.8964 (t80) cc_final: 0.8593 (t80) REVERT: J 34 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7926 (mt) REVERT: J 255 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6909 (t80) REVERT: K 100 LYS cc_start: 0.8662 (tptt) cc_final: 0.8435 (tptp) REVERT: Z 88 LEU cc_start: 0.8326 (mt) cc_final: 0.8097 (mp) REVERT: Z 102 GLN cc_start: 0.7906 (pm20) cc_final: 0.7691 (pm20) REVERT: D 3 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7369 (pmtt) REVERT: D 308 MET cc_start: 0.8993 (tpt) cc_final: 0.8786 (tpp) REVERT: N 95 TYR cc_start: 0.9153 (t80) cc_final: 0.8841 (t80) REVERT: E 126 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: E 152 LYS cc_start: 0.8632 (mttm) cc_final: 0.8333 (mttt) REVERT: E 261 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8047 (m-70) REVERT: E 375 LYS cc_start: 0.8315 (ttpp) cc_final: 0.8107 (ptmm) REVERT: E 412 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7897 (ttm170) REVERT: E 452 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8190 (ttp) REVERT: E 462 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6781 (pp30) REVERT: F 9 LYS cc_start: 0.6534 (mmtp) cc_final: 0.6317 (mmtm) REVERT: F 24 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7770 (mp) REVERT: F 137 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8765 (tpt) REVERT: F 184 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: G 86 MET cc_start: 0.6611 (tpp) cc_final: 0.6329 (mmt) REVERT: G 195 MET cc_start: 0.8248 (tpt) cc_final: 0.7414 (tpt) REVERT: G 208 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8317 (ttpp) outliers start: 52 outliers final: 33 residues processed: 454 average time/residue: 0.6227 time to fit residues: 324.8047 Evaluate side-chains 450 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 407 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 40 MET Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 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 87 SER Chi-restraints excluded: chain F residue 137 MET 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 Chi-restraints excluded: chain G residue 278 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 217 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 266 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 171 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.104787 restraints weight = 27768.335| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.17 r_work: 0.2653 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.403 24985 Z= 0.153 Angle : 0.803 41.002 34162 Z= 0.318 Chirality : 0.043 0.375 3592 Planarity : 0.005 0.057 4244 Dihedral : 10.223 106.409 3675 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.01 % Allowed : 21.68 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.15), residues: 2972 helix: 1.29 (0.13), residues: 1659 sheet: -2.14 (0.57), residues: 54 loop : 0.04 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 10 TYR 0.029 0.002 TYR G 72 PHE 0.019 0.001 PHE J 243 TRP 0.015 0.001 TRP D 147 HIS 0.007 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (24942) covalent geometry : angle 0.70141 / 0.31 (34151) SS BOND : bond 0.00220 / 0.12 ( 1) SS BOND : angle 2.48521 / 1.32 ( 2) hydrogen bonds : bond 0.04425 / 3.04 ( 1302) hydrogen bonds : angle 4.95359 / 3.58 ( 3741) metal coordination : bond 0.02486 / 1.07 ( 9) metal coordination : angle 24.09146 / 12.44 ( 9) Misc. bond : bond 0.16231 / 11.49 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9908.57 seconds wall clock time: 169 minutes 15.31 seconds (10155.31 seconds total)