Starting phenix.real_space_refine on Fri Nov 21 00:16:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s4k_24829/11_2025/7s4k_24829_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4k_24829/11_2025/7s4k_24829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s4k_24829/11_2025/7s4k_24829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4k_24829/11_2025/7s4k_24829.map" model { file = "/net/cci-nas-00/data/ceres_data/7s4k_24829/11_2025/7s4k_24829_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4k_24829/11_2025/7s4k_24829_trim.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19395 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15030 2.51 5 N 3417 2.21 5 O 4004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22589 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "K" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 284 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {' CU': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 284 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Restraints were copied for chains: E, I, F, J, G Time building chain proxies: 5.26, per 1000 atoms: 0.23 Number of scatterers: 22589 At special positions: 0 Unit cell: (107.194, 107.667, 118.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 O 4004 8.00 N 3417 7.00 C 15030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 279 " - pdb=" SG CYS G 279 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 908.1 milliseconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 21 sheets defined 53.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 184 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 375 through 382 removed outlier: 3.523A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 73 removed outlier: 3.501A pdb=" N PHE C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.663A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 114 Processing helix chain 'C' and resid 123 through 150 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 179 through 199 Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 219 through 233 removed outlier: 4.653A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 245 through 254 removed outlier: 3.783A pdb=" N LEU C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'B' and resid 10 through 43 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.843A pdb=" N TRP B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 55 Processing helix chain 'B' and resid 58 through 69 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 69 through 84 removed outlier: 3.867A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 107 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 140 through 155 removed outlier: 4.213A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.789A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 73 removed outlier: 3.501A pdb=" N PHE G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.664A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 114 Processing helix chain 'G' and resid 123 through 150 Processing helix chain 'G' and resid 150 through 163 Processing helix chain 'G' and resid 170 through 178 Processing helix chain 'G' and resid 179 through 199 Processing helix chain 'G' and resid 208 through 216 Processing helix chain 'G' and resid 219 through 233 removed outlier: 4.653A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 244 No H-bonds generated for 'chain 'G' and resid 242 through 244' Processing helix chain 'G' and resid 245 through 254 removed outlier: 3.783A pdb=" N LEU G 254 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 49 through 73 removed outlier: 3.501A pdb=" N PHE K 53 " --> pdb=" O LYS K 49 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.663A pdb=" N GLU K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 114 Processing helix chain 'K' and resid 123 through 150 Processing helix chain 'K' and resid 150 through 163 Processing helix chain 'K' and resid 170 through 178 Processing helix chain 'K' and resid 179 through 199 Processing helix chain 'K' and resid 208 through 216 Processing helix chain 'K' and resid 219 through 233 removed outlier: 4.653A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 242 through 244 No H-bonds generated for 'chain 'K' and resid 242 through 244' Processing helix chain 'K' and resid 245 through 254 removed outlier: 3.784A pdb=" N LEU K 254 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 208 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 231 through 257 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 375 through 382 removed outlier: 3.522A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 184 through 208 Processing helix chain 'I' and resid 212 through 221 Processing helix chain 'I' and resid 231 through 257 Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'I' and resid 375 through 382 removed outlier: 3.523A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 43 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.842A pdb=" N TRP F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 55 Processing helix chain 'F' and resid 58 through 69 Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 69 through 84 removed outlier: 3.868A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 140 through 155 removed outlier: 4.213A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 194 through 198 Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.789A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 43 Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.844A pdb=" N TRP J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 55 Processing helix chain 'J' and resid 58 through 69 Proline residue: J 65 - end of helix Processing helix chain 'J' and resid 69 through 84 removed outlier: 3.867A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 107 Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 124 through 137 Processing helix chain 'J' and resid 140 through 155 removed outlier: 4.212A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 165 Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'J' and resid 211 through 239 removed outlier: 3.788A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.343A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.722A pdb=" N VAL A 144 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE A 151 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET A 142 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 140 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 348 removed outlier: 5.843A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342 removed outlier: 5.273A pdb=" N LEU A 314 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE A 394 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA8, first strand: chain 'G' and resid 206 through 207 Processing sheet with id=AA9, first strand: chain 'K' and resid 206 through 207 Processing sheet with id=AB1, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.343A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.723A pdb=" N VAL E 144 " --> pdb=" O PRO E 149 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE E 151 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET E 142 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR E 140 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB4, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.843A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 341 through 342 removed outlier: 5.273A pdb=" N LEU E 314 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE E 394 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.343A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.722A pdb=" N VAL I 144 " --> pdb=" O PRO I 149 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE I 151 " --> pdb=" O MET I 142 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET I 142 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR I 140 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.843A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 341 through 342 removed outlier: 5.272A pdb=" N LEU I 314 " --> pdb=" O PHE I 394 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE I 394 " --> pdb=" O LEU I 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AC3, first strand: chain 'J' and resid 170 through 173 1140 hydrogen bonds defined for protein. 3321 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: 3.90 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3292 1.32 - 1.44: 6810 1.44 - 1.56: 12679 1.56 - 1.69: 166 1.69 - 1.81: 180 Bond restraints: 23127 Sorted by residual: bond pdb=" CB PLC J 303 " pdb=" O3 PLC J 303 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" CB PLC C 310 " pdb=" O3 PLC C 310 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" CB PLC G 301 " pdb=" O3 PLC G 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PLC B 301 " pdb=" O3 PLC B 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CB PLC F 302 " pdb=" O3 PLC F 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 4.00e+01 ... (remaining 23122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 30948 4.33 - 8.66: 282 8.66 - 12.99: 60 12.99 - 17.31: 0 17.31 - 21.64: 3 Bond angle restraints: 31293 Sorted by residual: angle pdb=" C9' PLC F 302 " pdb=" CA' PLC F 302 " pdb=" CB' PLC F 302 " ideal model delta sigma weight residual 112.96 134.60 -21.64 3.00e+00 1.11e-01 5.20e+01 angle pdb=" C9' PLC B 301 " pdb=" CA' PLC B 301 " pdb=" CB' PLC B 301 " ideal model delta sigma weight residual 112.96 134.58 -21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" C9' PLC J 305 " pdb=" CA' PLC J 305 " pdb=" CB' PLC J 305 " ideal model delta sigma weight residual 112.96 134.53 -21.57 3.00e+00 1.11e-01 5.17e+01 angle pdb=" CA HIS G 173 " pdb=" CB HIS G 173 " pdb=" CG HIS G 173 " ideal model delta sigma weight residual 113.80 120.87 -7.07 1.00e+00 1.00e+00 5.00e+01 angle pdb=" CA HIS K 173 " pdb=" CB HIS K 173 " pdb=" CG HIS K 173 " ideal model delta sigma weight residual 113.80 120.85 -7.05 1.00e+00 1.00e+00 4.97e+01 ... (remaining 31288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12596 34.45 - 68.90: 825 68.90 - 103.35: 72 103.35 - 137.80: 33 137.80 - 172.25: 21 Dihedral angle restraints: 13547 sinusoidal: 6095 harmonic: 7452 Sorted by residual: dihedral pdb=" CA GLN C 276 " pdb=" C GLN C 276 " pdb=" N SER C 277 " pdb=" CA SER C 277 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLN G 276 " pdb=" C GLN G 276 " pdb=" N SER G 277 " pdb=" CA SER G 277 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLN K 276 " pdb=" C GLN K 276 " pdb=" N SER K 277 " pdb=" CA SER K 277 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 13544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2340 0.048 - 0.096: 613 0.096 - 0.145: 199 0.145 - 0.193: 32 0.193 - 0.241: 23 Chirality restraints: 3207 Sorted by residual: chirality pdb=" C2 PLC K 305 " pdb=" C1 PLC K 305 " pdb=" C3 PLC K 305 " pdb=" O2 PLC K 305 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2 PLC G 307 " pdb=" C1 PLC G 307 " pdb=" C3 PLC G 307 " pdb=" O2 PLC G 307 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C2 PLC C 307 " pdb=" C1 PLC C 307 " pdb=" C3 PLC C 307 " pdb=" O2 PLC C 307 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 160 " 0.030 2.00e-02 2.50e+03 2.70e-02 1.09e+01 pdb=" CG HIS G 160 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS G 160 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS G 160 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS G 160 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS G 160 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 160 " -0.029 2.00e-02 2.50e+03 2.69e-02 1.09e+01 pdb=" CG HIS C 160 " 0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS C 160 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS C 160 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 160 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 160 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 160 " 0.029 2.00e-02 2.50e+03 2.68e-02 1.08e+01 pdb=" CG HIS K 160 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS K 160 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS K 160 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS K 160 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS K 160 " 0.021 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 21 2.14 - 2.83: 7097 2.83 - 3.52: 31953 3.52 - 4.21: 61849 4.21 - 4.90: 105713 Nonbonded interactions: 206633 Sorted by model distance: nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 301 " model vdw 1.448 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.448 2.320 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.448 2.320 nonbonded pdb=" ND1 HIS E 48 " pdb="CU CU E 502 " model vdw 1.975 2.320 nonbonded pdb=" ND1 HIS A 48 " pdb="CU CU A 502 " model vdw 1.976 2.320 ... (remaining 206628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'B' and resid 7 through 247) selection = (chain 'F' and resid 7 through 247) selection = (chain 'J' and resid 7 through 247) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 305)) selection = (chain 'G' and (resid 45 through 280 or resid 305)) selection = (chain 'K' and (resid 45 through 280 or resid 305)) } 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: 6.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 20.970 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 0.127 23127 Z= 0.469 Angle : 1.049 21.643 31294 Z= 0.524 Chirality : 0.052 0.241 3207 Planarity : 0.005 0.041 3732 Dihedral : 22.366 172.246 8787 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.37 % Rotamer: Outliers : 3.29 % Allowed : 18.24 % Favored : 78.46 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.71 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1185 sheet: 1.09 (0.31), residues: 333 loop : -0.29 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 117 TYR 0.021 0.001 TYR G 184 PHE 0.017 0.002 PHE J 31 TRP 0.018 0.001 TRP A 206 HIS 0.024 0.003 HIS I 33 Details of bonding type rmsd covalent geometry : bond 0.00899 (23127) covalent geometry : angle 1.04923 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.13096 ( 1140) hydrogen bonds : angle 6.62072 ( 3321) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 228 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: C 48 LYS cc_start: 0.7424 (ptmt) cc_final: 0.7139 (ptmm) REVERT: K 48 LYS cc_start: 0.7482 (ptmt) cc_final: 0.7238 (ptmm) REVERT: K 49 LYS cc_start: 0.6161 (pptt) cc_final: 0.5793 (pmtt) REVERT: K 117 ARG cc_start: 0.8516 (mmt-90) cc_final: 0.8247 (mmt90) REVERT: E 163 MET cc_start: 0.8938 (ttt) cc_final: 0.8709 (ttt) REVERT: I 163 MET cc_start: 0.8980 (ttt) cc_final: 0.8680 (ttt) REVERT: F 49 ASP cc_start: 0.8774 (t70) cc_final: 0.8474 (t70) REVERT: F 172 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8069 (tm-30) outliers start: 72 outliers final: 40 residues processed: 286 average time/residue: 0.7604 time to fit residues: 243.8203 Evaluate side-chains 254 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 180 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 118 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.081619 restraints weight = 28273.689| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.71 r_work: 0.2754 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23127 Z= 0.147 Angle : 0.605 7.022 31294 Z= 0.309 Chirality : 0.047 0.326 3207 Planarity : 0.005 0.042 3732 Dihedral : 22.506 178.862 4221 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.45 % Favored : 95.31 % Rotamer: Outliers : 2.74 % Allowed : 18.43 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.84 (0.17), residues: 2559 helix: 1.15 (0.15), residues: 1212 sheet: 0.59 (0.27), residues: 390 loop : -0.10 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 206 TYR 0.020 0.001 TYR C 184 PHE 0.017 0.001 PHE C 248 TRP 0.013 0.001 TRP C 112 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00315 (23127) covalent geometry : angle 0.60474 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04940 ( 1140) hydrogen bonds : angle 5.58772 ( 3321) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 0.751 Fit side-chains REVERT: A 112 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8733 (mtt90) REVERT: C 48 LYS cc_start: 0.7566 (ptmt) cc_final: 0.7255 (ptmm) REVERT: C 161 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7293 (mm110) REVERT: B 172 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8287 (tm-30) REVERT: B 206 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.8030 (mmm160) REVERT: G 48 LYS cc_start: 0.7623 (ptmt) cc_final: 0.7241 (ptmm) REVERT: K 48 LYS cc_start: 0.7587 (ptmt) cc_final: 0.7183 (ptmm) REVERT: K 117 ARG cc_start: 0.8253 (mmt-90) cc_final: 0.8046 (mmt90) REVERT: E 112 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8537 (mtt90) REVERT: I 123 ASP cc_start: 0.8807 (p0) cc_final: 0.8453 (p0) REVERT: I 163 MET cc_start: 0.9015 (ttt) cc_final: 0.8788 (ttt) REVERT: I 403 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.9009 (m) REVERT: F 172 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8449 (tm-30) REVERT: J 16 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8336 (tm-30) outliers start: 60 outliers final: 31 residues processed: 269 average time/residue: 0.7746 time to fit residues: 233.9465 Evaluate side-chains 245 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 180 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 207 optimal weight: 0.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN K 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.079666 restraints weight = 28301.157| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.70 r_work: 0.2719 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23127 Z= 0.173 Angle : 0.590 7.793 31294 Z= 0.307 Chirality : 0.046 0.230 3207 Planarity : 0.005 0.044 3732 Dihedral : 21.187 178.061 4195 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 3.38 % Allowed : 17.83 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2559 helix: 1.21 (0.15), residues: 1215 sheet: 0.56 (0.26), residues: 420 loop : -0.07 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 117 TYR 0.022 0.002 TYR G 184 PHE 0.019 0.002 PHE C 248 TRP 0.015 0.001 TRP F 231 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00389 (23127) covalent geometry : angle 0.59017 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.05005 ( 1140) hydrogen bonds : angle 5.40724 ( 3321) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 221 time to evaluate : 0.826 Fit side-chains REVERT: A 112 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8885 (mtt90) REVERT: C 48 LYS cc_start: 0.7508 (ptmt) cc_final: 0.7201 (ptmm) REVERT: B 172 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 206 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7948 (mtp85) REVERT: G 48 LYS cc_start: 0.7434 (ptmt) cc_final: 0.7132 (ptmm) REVERT: G 236 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7622 (mmp) REVERT: K 48 LYS cc_start: 0.7424 (ptmt) cc_final: 0.7054 (ptmm) REVERT: E 112 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8637 (mtt90) REVERT: E 237 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8437 (mtt) REVERT: I 112 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8223 (mtt90) REVERT: I 123 ASP cc_start: 0.8774 (p0) cc_final: 0.8422 (p0) REVERT: F 172 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8419 (tm-30) REVERT: J 16 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: J 207 THR cc_start: 0.8352 (m) cc_final: 0.8109 (m) outliers start: 74 outliers final: 36 residues processed: 275 average time/residue: 0.7350 time to fit residues: 227.9344 Evaluate side-chains 256 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 135 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 251 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.080926 restraints weight = 28415.649| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.71 r_work: 0.2746 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23127 Z= 0.138 Angle : 0.560 7.887 31294 Z= 0.289 Chirality : 0.045 0.252 3207 Planarity : 0.004 0.043 3732 Dihedral : 20.127 177.558 4179 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.43 % Rotamer: Outliers : 2.97 % Allowed : 17.56 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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 (0.17), residues: 2559 helix: 1.32 (0.15), residues: 1209 sheet: 0.62 (0.26), residues: 417 loop : -0.02 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 206 TYR 0.021 0.001 TYR G 184 PHE 0.017 0.001 PHE C 248 TRP 0.013 0.001 TRP F 231 HIS 0.003 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00303 (23127) covalent geometry : angle 0.56007 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04587 ( 1140) hydrogen bonds : angle 5.27762 ( 3321) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 219 time to evaluate : 0.868 Fit side-chains REVERT: A 112 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8946 (mtt90) REVERT: C 46 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7648 (mp) REVERT: C 48 LYS cc_start: 0.7439 (ptmt) cc_final: 0.7150 (ptmm) REVERT: B 47 ASP cc_start: 0.8796 (m-30) cc_final: 0.8580 (m-30) REVERT: B 172 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8268 (tm-30) REVERT: G 48 LYS cc_start: 0.7397 (ptmt) cc_final: 0.7098 (ptmm) REVERT: K 46 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7690 (mp) REVERT: K 48 LYS cc_start: 0.7454 (ptmt) cc_final: 0.7155 (ptmm) REVERT: E 112 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8878 (mtt90) REVERT: I 112 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8173 (mtt90) REVERT: I 123 ASP cc_start: 0.8749 (p0) cc_final: 0.8407 (p0) REVERT: F 172 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8351 (tm-30) REVERT: J 16 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: J 150 MET cc_start: 0.8762 (tpt) cc_final: 0.8548 (tpt) outliers start: 65 outliers final: 38 residues processed: 268 average time/residue: 0.7455 time to fit residues: 224.6570 Evaluate side-chains 260 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 53 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 235 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN G 161 GLN K 161 GLN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.078226 restraints weight = 27985.206| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.68 r_work: 0.2691 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23127 Z= 0.208 Angle : 0.612 8.392 31294 Z= 0.319 Chirality : 0.047 0.250 3207 Planarity : 0.005 0.046 3732 Dihedral : 19.735 177.860 4179 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.35 % Rotamer: Outliers : 3.48 % Allowed : 17.38 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2559 helix: 1.26 (0.15), residues: 1212 sheet: 0.50 (0.26), residues: 420 loop : -0.07 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 206 TYR 0.023 0.002 TYR C 184 PHE 0.020 0.002 PHE C 248 TRP 0.015 0.001 TRP F 152 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00473 (23127) covalent geometry : angle 0.61230 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.05190 ( 1140) hydrogen bonds : angle 5.39501 ( 3321) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 218 time to evaluate : 0.886 Fit side-chains REVERT: A 112 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.8892 (mtt90) REVERT: C 46 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7658 (mp) REVERT: C 48 LYS cc_start: 0.7464 (ptmt) cc_final: 0.7178 (ptmm) REVERT: B 172 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8320 (tm-30) REVERT: G 48 LYS cc_start: 0.7412 (ptmt) cc_final: 0.7114 (ptmm) REVERT: K 46 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7656 (mp) REVERT: K 48 LYS cc_start: 0.7411 (ptmt) cc_final: 0.7107 (ptmm) REVERT: K 113 LYS cc_start: 0.8712 (mptt) cc_final: 0.8347 (ttpt) REVERT: E 112 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8715 (mtt90) REVERT: I 112 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8323 (mtt90) REVERT: F 172 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8408 (tm-30) outliers start: 76 outliers final: 45 residues processed: 271 average time/residue: 0.7220 time to fit residues: 221.0165 Evaluate side-chains 261 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 112 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 161 GLN K 161 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.078642 restraints weight = 28358.485| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.69 r_work: 0.2701 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23127 Z= 0.185 Angle : 0.594 8.483 31294 Z= 0.308 Chirality : 0.047 0.247 3207 Planarity : 0.005 0.046 3732 Dihedral : 19.374 176.374 4178 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.42 % Favored : 95.39 % Rotamer: Outliers : 3.43 % Allowed : 17.19 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2559 helix: 1.27 (0.15), residues: 1209 sheet: 0.51 (0.26), residues: 420 loop : -0.09 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 206 TYR 0.021 0.002 TYR K 184 PHE 0.018 0.002 PHE C 248 TRP 0.014 0.001 TRP F 231 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00420 (23127) covalent geometry : angle 0.59358 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04974 ( 1140) hydrogen bonds : angle 5.35820 ( 3321) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 209 time to evaluate : 0.866 Fit side-chains REVERT: A 112 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.8194 (mtt90) REVERT: C 46 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7643 (mp) REVERT: C 48 LYS cc_start: 0.7404 (ptmt) cc_final: 0.7130 (ptmm) REVERT: B 172 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8252 (tm-30) REVERT: G 48 LYS cc_start: 0.7370 (ptmt) cc_final: 0.7092 (ptmm) REVERT: K 48 LYS cc_start: 0.7379 (ptmt) cc_final: 0.7089 (ptmm) REVERT: K 113 LYS cc_start: 0.8701 (mptt) cc_final: 0.8355 (ttpt) REVERT: E 112 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8650 (mtt90) REVERT: I 112 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8320 (mtt90) REVERT: F 172 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8384 (tm-30) REVERT: J 198 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8759 (ttp-170) outliers start: 75 outliers final: 47 residues processed: 264 average time/residue: 0.7183 time to fit residues: 213.8467 Evaluate side-chains 260 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 198 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 57 optimal weight: 20.0000 chunk 98 optimal weight: 0.6980 chunk 249 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN K 161 GLN I 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.080083 restraints weight = 28227.713| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.70 r_work: 0.2731 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23127 Z= 0.143 Angle : 0.567 8.465 31294 Z= 0.293 Chirality : 0.045 0.231 3207 Planarity : 0.004 0.044 3732 Dihedral : 18.703 173.217 4178 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.14 % Favored : 95.66 % Rotamer: Outliers : 2.88 % Allowed : 17.92 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2559 helix: 1.32 (0.15), residues: 1212 sheet: 0.59 (0.26), residues: 417 loop : -0.04 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 117 TYR 0.021 0.001 TYR G 184 PHE 0.017 0.001 PHE C 248 TRP 0.014 0.001 TRP F 231 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00319 (23127) covalent geometry : angle 0.56742 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04651 ( 1140) hydrogen bonds : angle 5.26730 ( 3321) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 0.889 Fit side-chains REVERT: A 112 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.8878 (mtt90) REVERT: C 46 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7583 (mp) REVERT: C 48 LYS cc_start: 0.7378 (ptmt) cc_final: 0.7115 (ptmm) REVERT: B 172 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8243 (tm-30) REVERT: G 48 LYS cc_start: 0.7355 (ptmt) cc_final: 0.7086 (ptmm) REVERT: K 48 LYS cc_start: 0.7312 (ptmt) cc_final: 0.7036 (ptmm) REVERT: K 113 LYS cc_start: 0.8698 (mptt) cc_final: 0.8341 (ttpt) REVERT: E 112 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8629 (mtt90) REVERT: E 404 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: I 112 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8319 (mtt90) REVERT: I 123 ASP cc_start: 0.8739 (p0) cc_final: 0.8388 (p0) REVERT: F 172 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8346 (tm-30) REVERT: J 198 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8744 (ttp-170) outliers start: 63 outliers final: 47 residues processed: 262 average time/residue: 0.7231 time to fit residues: 213.9644 Evaluate side-chains 262 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain J residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 227 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 161 GLN K 161 GLN I 108 GLN J 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.081375 restraints weight = 28103.180| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.71 r_work: 0.2757 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23127 Z= 0.125 Angle : 0.551 8.370 31294 Z= 0.283 Chirality : 0.045 0.221 3207 Planarity : 0.004 0.043 3732 Dihedral : 18.157 170.279 4178 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 2.65 % Allowed : 18.52 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 1.08 (0.17), residues: 2559 helix: 1.37 (0.15), residues: 1215 sheet: 0.62 (0.26), residues: 417 loop : 0.02 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 206 TYR 0.021 0.001 TYR G 184 PHE 0.016 0.001 PHE C 248 TRP 0.013 0.001 TRP I 202 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00271 (23127) covalent geometry : angle 0.55130 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04419 ( 1140) hydrogen bonds : angle 5.19349 ( 3321) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.925 Fit side-chains REVERT: A 112 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8961 (mtt90) REVERT: C 46 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7577 (mp) REVERT: C 48 LYS cc_start: 0.7389 (ptmt) cc_final: 0.7132 (ptmm) REVERT: B 47 ASP cc_start: 0.8830 (m-30) cc_final: 0.8558 (m-30) REVERT: B 172 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8222 (tm-30) REVERT: G 48 LYS cc_start: 0.7312 (ptmt) cc_final: 0.7059 (ptmm) REVERT: K 48 LYS cc_start: 0.7279 (ptmt) cc_final: 0.7012 (ptmm) REVERT: E 112 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8855 (mtt90) REVERT: E 208 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7947 (mtm180) REVERT: E 404 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: I 112 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8255 (mtt90) REVERT: I 123 ASP cc_start: 0.8696 (p0) cc_final: 0.8361 (p0) REVERT: F 172 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8299 (tm-30) REVERT: J 198 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8736 (ttp-170) outliers start: 58 outliers final: 45 residues processed: 261 average time/residue: 0.7356 time to fit residues: 216.8874 Evaluate side-chains 261 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 198 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 199 optimal weight: 0.5980 chunk 167 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN G 161 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.082512 restraints weight = 28564.063| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.73 r_work: 0.2779 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23127 Z= 0.117 Angle : 0.544 8.149 31294 Z= 0.278 Chirality : 0.044 0.208 3207 Planarity : 0.004 0.043 3732 Dihedral : 17.594 167.058 4178 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.34 % Favored : 95.47 % Rotamer: Outliers : 2.38 % Allowed : 18.79 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 1.17 (0.17), residues: 2559 helix: 1.44 (0.15), residues: 1218 sheet: 0.70 (0.26), residues: 417 loop : 0.05 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 206 TYR 0.021 0.001 TYR G 184 PHE 0.016 0.001 PHE C 248 TRP 0.014 0.001 TRP I 202 HIS 0.004 0.001 HIS G 173 Details of bonding type rmsd covalent geometry : bond 0.00251 (23127) covalent geometry : angle 0.54415 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04293 ( 1140) hydrogen bonds : angle 5.13090 ( 3321) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.946 Fit side-chains REVERT: A 112 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8924 (mtt90) REVERT: C 46 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7596 (mp) REVERT: C 48 LYS cc_start: 0.7357 (ptmt) cc_final: 0.7100 (ptmm) REVERT: B 47 ASP cc_start: 0.8834 (m-30) cc_final: 0.8557 (m-30) REVERT: B 172 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8194 (tm-30) REVERT: G 48 LYS cc_start: 0.7244 (ptmt) cc_final: 0.6990 (ptmm) REVERT: K 48 LYS cc_start: 0.7201 (ptmt) cc_final: 0.6957 (ptmm) REVERT: E 112 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8817 (mtt180) REVERT: E 401 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8285 (mt0) REVERT: I 112 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8173 (mtt90) REVERT: I 123 ASP cc_start: 0.8668 (p0) cc_final: 0.8338 (p0) REVERT: F 172 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8261 (tm-30) outliers start: 52 outliers final: 34 residues processed: 261 average time/residue: 0.7422 time to fit residues: 218.1324 Evaluate side-chains 251 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 202 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN G 161 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN K 161 GLN I 401 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.077709 restraints weight = 28401.210| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.71 r_work: 0.2685 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23127 Z= 0.234 Angle : 0.622 8.686 31294 Z= 0.323 Chirality : 0.048 0.237 3207 Planarity : 0.005 0.047 3732 Dihedral : 17.881 168.038 4174 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.42 % Favored : 95.39 % Rotamer: Outliers : 2.19 % Allowed : 19.20 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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 (0.17), residues: 2559 helix: 1.33 (0.15), residues: 1209 sheet: 0.65 (0.26), residues: 414 loop : -0.04 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 117 TYR 0.023 0.002 TYR C 184 PHE 0.021 0.002 PHE E 74 TRP 0.015 0.002 TRP F 152 HIS 0.005 0.001 HIS K 160 Details of bonding type rmsd covalent geometry : bond 0.00540 (23127) covalent geometry : angle 0.62186 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.05241 ( 1140) hydrogen bonds : angle 5.37185 ( 3321) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 0.884 Fit side-chains REVERT: A 112 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8559 (mtt90) REVERT: C 46 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7687 (mp) REVERT: C 48 LYS cc_start: 0.7425 (ptmt) cc_final: 0.7159 (ptmm) REVERT: G 48 LYS cc_start: 0.7287 (ptmt) cc_final: 0.7016 (ptmm) REVERT: K 48 LYS cc_start: 0.7304 (ptmt) cc_final: 0.7030 (ptmm) REVERT: E 112 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8760 (mtt90) REVERT: I 112 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8371 (mtt90) outliers start: 48 outliers final: 33 residues processed: 244 average time/residue: 0.7818 time to fit residues: 213.5903 Evaluate side-chains 245 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 127 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.080920 restraints weight = 28750.464| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.73 r_work: 0.2745 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23127 Z= 0.127 Angle : 0.557 8.287 31294 Z= 0.287 Chirality : 0.045 0.212 3207 Planarity : 0.004 0.046 3732 Dihedral : 17.465 164.980 4174 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.22 % Favored : 95.58 % Rotamer: Outliers : 1.97 % Allowed : 19.20 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 1.13 (0.17), residues: 2559 helix: 1.40 (0.15), residues: 1212 sheet: 0.70 (0.26), residues: 411 loop : 0.04 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 117 TYR 0.022 0.001 TYR G 184 PHE 0.015 0.001 PHE C 248 TRP 0.014 0.001 TRP F 231 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00278 (23127) covalent geometry : angle 0.55655 (31293) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04486 ( 1140) hydrogen bonds : angle 5.22739 ( 3321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8715.53 seconds wall clock time: 148 minutes 50.59 seconds (8930.59 seconds total)