Starting phenix.real_space_refine on Sat Mar 7 09:40:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s4i_24827/03_2026/7s4i_24827_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4i_24827/03_2026/7s4i_24827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s4i_24827/03_2026/7s4i_24827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4i_24827/03_2026/7s4i_24827.map" model { file = "/net/cci-nas-00/data/ceres_data/7s4i_24827/03_2026/7s4i_24827_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4i_24827/03_2026/7s4i_24827_trim.cif" } resolution = 2.26 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 4249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22834 Number of models: 1 Model: "" Number of chains: 27 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: "G" 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: "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: "E" 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: "I" 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: "F" 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: "J" 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: "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: 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: "G" 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: "K" 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: "E" 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: "I" 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: "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: 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 5.08, per 1000 atoms: 0.22 Number of scatterers: 22834 At special positions: 0 Unit cell: (106.722, 107.194, 119, 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 4249 8.00 N 3417 7.00 C 15030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.51 Conformation dependent library (CDL) restraints added in 879.3 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: 96 helices and 18 sheets defined 53.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 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 376 through 382 removed outlier: 3.671A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 73 removed outlier: 3.906A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.624A 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 161 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 179 through 199 Processing helix chain 'C' and resid 207 through 233 Proline residue: C 217 - end of helix removed outlier: 3.578A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.662A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS C 231 " --> pdb=" O ASN C 227 " (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: 3.698A 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: 3.673A pdb=" N TRP B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) 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: 3.958A 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: 4.109A 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: 3.765A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 73 removed outlier: 3.906A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.624A 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 161 Processing helix chain 'G' and resid 170 through 177 Processing helix chain 'G' and resid 179 through 199 Processing helix chain 'G' and resid 207 through 233 Proline residue: G 217 - end of helix removed outlier: 3.578A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.662A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS G 231 " --> pdb=" O ASN G 227 " (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: 3.699A 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: 3.906A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.624A 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 161 Processing helix chain 'K' and resid 170 through 177 Processing helix chain 'K' and resid 179 through 199 Processing helix chain 'K' and resid 207 through 233 Proline residue: K 217 - end of helix removed outlier: 3.579A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.663A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS K 231 " --> pdb=" O ASN K 227 " (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: 3.698A 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 376 through 382 removed outlier: 3.672A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.629A 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 376 through 382 removed outlier: 3.672A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.629A 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: 3.672A pdb=" N TRP F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) 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: 3.959A 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: 4.110A 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: 3.765A 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: 3.673A pdb=" N TRP J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) 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: 3.958A 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: 4.108A 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: 3.764A 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: 4.295A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 108 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.671A pdb=" N VAL A 144 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE A 151 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET A 142 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.828A 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: 5.814A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.253A 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: 6.555A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA7, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.296A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.671A pdb=" N VAL E 144 " --> pdb=" O PRO E 149 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE E 151 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET E 142 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR E 140 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB1, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.814A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 341 through 342 removed outlier: 6.555A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.295A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.671A pdb=" N VAL I 144 " --> pdb=" O PRO I 149 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE I 151 " --> pdb=" O MET I 142 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET I 142 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR I 140 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.814A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 341 through 342 removed outlier: 6.555A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AB9, first strand: chain 'J' and resid 170 through 173 1116 hydrogen bonds defined for protein. 3276 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: 3.73 Time building geometry restraints manager: 1.92 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: 3302 1.32 - 1.44: 6807 1.44 - 1.57: 12698 1.57 - 1.69: 140 1.69 - 1.81: 180 Bond restraints: 23127 Sorted by residual: bond pdb=" CB PLC K 301 " pdb=" O3 PLC K 301 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.07e+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 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 4.01e+01 bond pdb=" CB PLC G 303 " pdb=" O3 PLC G 303 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" CB PLC C 302 " pdb=" O3 PLC C 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 23122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 29767 2.12 - 4.24: 1168 4.24 - 6.37: 235 6.37 - 8.49: 45 8.49 - 10.61: 78 Bond angle restraints: 31293 Sorted by residual: angle pdb=" N THR G 232 " pdb=" CA THR G 232 " pdb=" C THR G 232 " ideal model delta sigma weight residual 111.03 104.44 6.59 1.11e+00 8.12e-01 3.52e+01 angle pdb=" N THR C 232 " pdb=" CA THR C 232 " pdb=" C THR C 232 " ideal model delta sigma weight residual 111.03 104.48 6.55 1.11e+00 8.12e-01 3.48e+01 angle pdb=" N THR K 232 " pdb=" CA THR K 232 " pdb=" C THR K 232 " ideal model delta sigma weight residual 111.03 104.49 6.54 1.11e+00 8.12e-01 3.47e+01 angle pdb=" N LEU I 376 " pdb=" CA LEU I 376 " pdb=" C LEU I 376 " ideal model delta sigma weight residual 112.89 107.12 5.77 1.24e+00 6.50e-01 2.17e+01 angle pdb=" N LEU E 376 " pdb=" CA LEU E 376 " pdb=" C LEU E 376 " ideal model delta sigma weight residual 112.89 107.12 5.77 1.24e+00 6.50e-01 2.17e+01 ... (remaining 31288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12582 34.45 - 68.89: 819 68.89 - 103.34: 96 103.34 - 137.78: 36 137.78 - 172.23: 12 Dihedral angle restraints: 13545 sinusoidal: 6093 harmonic: 7452 Sorted by residual: dihedral pdb=" O2 PLC K 301 " pdb=" C1 PLC K 301 " pdb=" C2 PLC K 301 " pdb=" O3P PLC K 301 " ideal model delta sinusoidal sigma weight residual -55.71 116.52 -172.23 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC G 301 " pdb=" C1 PLC G 301 " pdb=" C2 PLC G 301 " pdb=" O3P PLC G 301 " ideal model delta sinusoidal sigma weight residual -55.71 116.52 -172.23 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC C 310 " pdb=" C1 PLC C 310 " pdb=" C2 PLC C 310 " pdb=" O3P PLC C 310 " ideal model delta sinusoidal sigma weight residual -55.71 116.50 -172.21 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2376 0.049 - 0.099: 647 0.099 - 0.148: 148 0.148 - 0.198: 25 0.198 - 0.247: 11 Chirality restraints: 3207 Sorted by residual: 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 -2.56 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C2 PLC G 308 " pdb=" C1 PLC G 308 " pdb=" C3 PLC G 308 " pdb=" O2 PLC G 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.56 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2 PLC K 308 " pdb=" C1 PLC K 308 " pdb=" C3 PLC K 308 " pdb=" O2 PLC K 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.56 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 34 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C GLY E 34 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY E 34 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU E 35 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 34 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C GLY A 34 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY A 34 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 35 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 34 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLY I 34 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY I 34 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU I 35 " 0.010 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 16 2.14 - 2.83: 7310 2.83 - 3.52: 33786 3.52 - 4.21: 64169 4.21 - 4.90: 107395 Nonbonded interactions: 212676 Sorted by model distance: nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.450 2.320 nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 302 " model vdw 1.451 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.451 2.320 nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU E 501 " model vdw 1.967 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.968 2.320 ... (remaining 212671 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 305 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 309)) selection = (chain 'G' and (resid 45 through 280 or resid 309)) selection = (chain 'K' and (resid 45 through 280 or resid 309)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.340 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.008 0.128 23127 Z= 0.440 Angle : 1.010 10.610 31293 Z= 0.478 Chirality : 0.049 0.247 3207 Planarity : 0.005 0.043 3732 Dihedral : 22.635 172.228 8787 Min Nonbonded Distance : 1.450 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.24 % Favored : 94.29 % Rotamer: Outliers : 3.29 % Allowed : 18.06 % Favored : 78.65 % 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: 0.83 (0.17), residues: 2559 helix: 1.19 (0.15), residues: 1200 sheet: 1.30 (0.28), residues: 357 loop : -0.45 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 117 TYR 0.021 0.001 TYR C 184 PHE 0.015 0.001 PHE J 31 TRP 0.017 0.002 TRP A 202 HIS 0.021 0.002 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00841 (23127) covalent geometry : angle 1.01025 (31293) hydrogen bonds : bond 0.11523 ( 1116) hydrogen bonds : angle 6.17656 ( 3276) *********************** 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 322 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 250 time to evaluate : 0.758 Fit side-chains REVERT: A 108 GLN cc_start: 0.8068 (pt0) cc_final: 0.7772 (pp30) REVERT: C 45 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6374 (mt) REVERT: G 45 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6384 (mt) REVERT: K 45 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6384 (mt) REVERT: E 108 GLN cc_start: 0.8056 (pt0) cc_final: 0.7772 (pp30) REVERT: I 108 GLN cc_start: 0.8039 (pt0) cc_final: 0.7739 (pp30) REVERT: I 399 ASN cc_start: 0.7495 (p0) cc_final: 0.7290 (p0) REVERT: J 172 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7752 (tp30) outliers start: 72 outliers final: 39 residues processed: 313 average time/residue: 0.7134 time to fit residues: 251.3213 Evaluate side-chains 273 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 240 PHE 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 138 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 231 HIS Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 138 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN G 118 ASN K 118 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.095566 restraints weight = 24436.984| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.20 r_work: 0.2971 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23127 Z= 0.178 Angle : 0.653 7.447 31293 Z= 0.337 Chirality : 0.048 0.365 3207 Planarity : 0.005 0.041 3732 Dihedral : 22.414 176.736 4211 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.08 % Favored : 94.80 % Rotamer: Outliers : 3.06 % Allowed : 17.24 % Favored : 79.70 % 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: 0.88 (0.17), residues: 2559 helix: 1.09 (0.15), residues: 1215 sheet: 0.73 (0.27), residues: 390 loop : 0.01 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 117 TYR 0.022 0.002 TYR G 184 PHE 0.018 0.002 PHE B 31 TRP 0.035 0.002 TRP G 234 HIS 0.005 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00382 (23127) covalent geometry : angle 0.65281 (31293) hydrogen bonds : bond 0.05408 ( 1116) hydrogen bonds : angle 5.40431 ( 3276) *********************** 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 293 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 226 time to evaluate : 0.896 Fit side-chains REVERT: A 108 GLN cc_start: 0.8382 (pt0) cc_final: 0.8055 (pp30) REVERT: A 299 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7508 (ptm-80) REVERT: A 316 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: G 48 LYS cc_start: 0.7532 (ptmt) cc_final: 0.7325 (ptmt) REVERT: E 108 GLN cc_start: 0.8358 (pt0) cc_final: 0.8105 (pp30) REVERT: E 316 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: I 108 GLN cc_start: 0.8336 (pt0) cc_final: 0.8043 (pp30) REVERT: I 163 MET cc_start: 0.8831 (ttt) cc_final: 0.8594 (ttt) REVERT: I 299 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7426 (ptm-80) REVERT: J 13 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: J 172 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8060 (tp30) outliers start: 67 outliers final: 31 residues processed: 279 average time/residue: 0.7146 time to fit residues: 224.1634 Evaluate side-chains 256 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 231 HIS Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU 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 J residue 13 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 161 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 247 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 118 ASN ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 168 ASN I 404 GLN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.094526 restraints weight = 24516.711| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.18 r_work: 0.2946 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23127 Z= 0.197 Angle : 0.651 7.939 31293 Z= 0.341 Chirality : 0.048 0.276 3207 Planarity : 0.005 0.039 3732 Dihedral : 21.404 175.463 4173 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.88 % Favored : 95.00 % Rotamer: Outliers : 3.61 % Allowed : 15.78 % Favored : 80.61 % 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: 0.76 (0.17), residues: 2559 helix: 1.07 (0.15), residues: 1236 sheet: 0.84 (0.28), residues: 339 loop : -0.23 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 117 TYR 0.023 0.002 TYR G 184 PHE 0.020 0.002 PHE B 31 TRP 0.018 0.002 TRP J 231 HIS 0.005 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00434 (23127) covalent geometry : angle 0.65058 (31293) hydrogen bonds : bond 0.05550 ( 1116) hydrogen bonds : angle 5.38487 ( 3276) *********************** 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 305 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 226 time to evaluate : 0.541 Fit side-chains REVERT: A 299 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7515 (ptm-80) REVERT: A 316 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: C 45 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6815 (mt) REVERT: B 13 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: E 299 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7382 (ptm-80) REVERT: E 316 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: I 299 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7536 (ptm-80) REVERT: I 316 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: F 13 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: J 13 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8226 (tt0) outliers start: 79 outliers final: 31 residues processed: 287 average time/residue: 0.7458 time to fit residues: 239.9882 Evaluate side-chains 258 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL 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 105 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 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 217 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.094562 restraints weight = 24623.190| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.20 r_work: 0.2944 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23127 Z= 0.194 Angle : 0.644 8.520 31293 Z= 0.336 Chirality : 0.048 0.285 3207 Planarity : 0.005 0.039 3732 Dihedral : 21.056 174.223 4159 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 3.57 % Allowed : 16.05 % Favored : 80.38 % 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: 0.78 (0.17), residues: 2559 helix: 1.09 (0.15), residues: 1221 sheet: 0.83 (0.28), residues: 339 loop : -0.19 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 117 TYR 0.022 0.002 TYR G 184 PHE 0.020 0.002 PHE B 31 TRP 0.017 0.002 TRP J 231 HIS 0.005 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00429 (23127) covalent geometry : angle 0.64365 (31293) hydrogen bonds : bond 0.05458 ( 1116) hydrogen bonds : angle 5.36332 ( 3276) *********************** 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 307 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 229 time to evaluate : 0.832 Fit side-chains REVERT: A 112 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8493 (mtt180) REVERT: A 299 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7507 (ptm-80) REVERT: A 316 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: C 45 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6788 (mt) REVERT: B 13 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: G 45 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6741 (mt) REVERT: K 45 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6714 (mt) REVERT: E 108 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8080 (pp30) REVERT: E 112 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8553 (mtt180) REVERT: E 299 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7262 (ptm-80) REVERT: E 316 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: I 108 GLN cc_start: 0.8371 (pt0) cc_final: 0.8070 (pp30) REVERT: I 112 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8572 (mtt180) REVERT: I 299 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7538 (ptm-80) REVERT: I 316 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: F 13 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: J 13 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8245 (tt0) outliers start: 78 outliers final: 35 residues processed: 290 average time/residue: 0.7251 time to fit residues: 235.7565 Evaluate side-chains 270 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 13 GLU 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 33 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.095596 restraints weight = 24371.706| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.16 r_work: 0.2958 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23127 Z= 0.169 Angle : 0.617 8.130 31293 Z= 0.322 Chirality : 0.046 0.269 3207 Planarity : 0.005 0.039 3732 Dihedral : 20.762 176.624 4157 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.00 % Favored : 94.88 % Rotamer: Outliers : 3.93 % Allowed : 15.73 % Favored : 80.34 % 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: 0.83 (0.17), residues: 2559 helix: 1.12 (0.15), residues: 1224 sheet: 0.84 (0.28), residues: 339 loop : -0.15 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 117 TYR 0.022 0.002 TYR G 184 PHE 0.018 0.002 PHE B 31 TRP 0.016 0.002 TRP J 231 HIS 0.004 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00370 (23127) covalent geometry : angle 0.61655 (31293) hydrogen bonds : bond 0.05236 ( 1116) hydrogen bonds : angle 5.29925 ( 3276) *********************** 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 316 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 230 time to evaluate : 0.565 Fit side-chains REVERT: A 112 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8481 (mtt180) REVERT: A 299 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7479 (ptm-80) REVERT: A 316 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: C 45 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6748 (mt) REVERT: B 13 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: G 45 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6696 (mt) REVERT: K 45 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6687 (mt) REVERT: E 108 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: E 112 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8512 (mtt180) REVERT: E 299 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7282 (ptm-80) REVERT: E 316 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: I 108 GLN cc_start: 0.8357 (pt0) cc_final: 0.8049 (pp30) REVERT: I 112 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8539 (mtt180) REVERT: I 299 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7531 (ptm-80) REVERT: I 316 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: F 13 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8419 (tt0) outliers start: 86 outliers final: 42 residues processed: 300 average time/residue: 0.7143 time to fit residues: 241.0219 Evaluate side-chains 274 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 153 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 57 optimal weight: 6.9990 chunk 167 optimal weight: 0.0060 chunk 32 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.9298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.098078 restraints weight = 24641.736| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.18 r_work: 0.3007 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23127 Z= 0.127 Angle : 0.577 8.182 31293 Z= 0.299 Chirality : 0.045 0.254 3207 Planarity : 0.004 0.039 3732 Dihedral : 20.165 179.862 4157 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.65 % Rotamer: Outliers : 2.79 % Allowed : 16.92 % Favored : 80.29 % 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: 0.82 (0.17), residues: 2559 helix: 1.21 (0.15), residues: 1206 sheet: 0.68 (0.28), residues: 354 loop : -0.23 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 115 TYR 0.021 0.001 TYR C 184 PHE 0.016 0.001 PHE B 31 TRP 0.015 0.001 TRP I 206 HIS 0.003 0.001 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00267 (23127) covalent geometry : angle 0.57738 (31293) hydrogen bonds : bond 0.04716 ( 1116) hydrogen bonds : angle 5.15396 ( 3276) *********************** 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 296 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 0.811 Fit side-chains REVERT: A 112 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8440 (mtt180) REVERT: A 299 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7508 (ptm-80) REVERT: A 316 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: C 235 PHE cc_start: 0.6831 (m-80) cc_final: 0.6619 (m-80) REVERT: B 13 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: B 245 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7792 (mm110) REVERT: E 112 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8452 (mtt180) REVERT: E 299 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7325 (ptm-80) REVERT: I 108 GLN cc_start: 0.8280 (pt0) cc_final: 0.7983 (pp30) REVERT: I 112 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8467 (mtt180) REVERT: I 299 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7463 (ptm-80) REVERT: I 316 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: F 13 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: J 245 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7853 (mm110) outliers start: 61 outliers final: 36 residues processed: 284 average time/residue: 0.7291 time to fit residues: 232.6216 Evaluate side-chains 269 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 123 THR 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 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL 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 316 GLU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.093685 restraints weight = 24474.670| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.19 r_work: 0.2926 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1581 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= 0.225 Angle : 0.663 8.790 31293 Z= 0.348 Chirality : 0.048 0.271 3207 Planarity : 0.005 0.041 3732 Dihedral : 20.365 176.553 4157 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % Rotamer: Outliers : 3.29 % Allowed : 16.32 % Favored : 80.38 % 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: 0.84 (0.17), residues: 2559 helix: 1.11 (0.15), residues: 1224 sheet: 0.83 (0.28), residues: 339 loop : -0.11 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 115 TYR 0.024 0.002 TYR G 184 PHE 0.022 0.002 PHE G 248 TRP 0.017 0.002 TRP F 231 HIS 0.006 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00502 (23127) covalent geometry : angle 0.66316 (31293) hydrogen bonds : bond 0.05663 ( 1116) hydrogen bonds : angle 5.37275 ( 3276) *********************** 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 292 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 220 time to evaluate : 0.751 Fit side-chains REVERT: A 112 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8542 (mtt180) REVERT: A 299 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7463 (ptm-80) REVERT: A 316 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: B 13 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: E 112 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8558 (mtt180) REVERT: E 299 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7259 (ptm-80) REVERT: E 316 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: I 112 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8588 (mtt180) REVERT: I 299 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7494 (ptm-80) REVERT: I 316 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: I 399 ASN cc_start: 0.7707 (p0) cc_final: 0.7474 (p0) REVERT: F 13 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8426 (tt0) outliers start: 72 outliers final: 42 residues processed: 277 average time/residue: 0.7267 time to fit residues: 225.9992 Evaluate side-chains 265 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL 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 316 GLU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 99 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 233 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096590 restraints weight = 24475.862| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.20 r_work: 0.2980 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23127 Z= 0.139 Angle : 0.597 7.838 31293 Z= 0.310 Chirality : 0.045 0.254 3207 Planarity : 0.004 0.040 3732 Dihedral : 19.923 178.894 4157 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.04 % Favored : 94.84 % Rotamer: Outliers : 2.70 % Allowed : 16.92 % Favored : 80.38 % 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: 0.84 (0.17), residues: 2559 helix: 1.17 (0.15), residues: 1218 sheet: 0.86 (0.28), residues: 339 loop : -0.21 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 115 TYR 0.022 0.001 TYR C 184 PHE 0.017 0.001 PHE B 31 TRP 0.015 0.001 TRP J 231 HIS 0.004 0.001 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00297 (23127) covalent geometry : angle 0.59701 (31293) hydrogen bonds : bond 0.04927 ( 1116) hydrogen bonds : angle 5.22599 ( 3276) *********************** 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 284 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 0.767 Fit side-chains REVERT: A 112 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8446 (mtt180) REVERT: A 299 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7465 (ptm-80) REVERT: A 316 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: C 235 PHE cc_start: 0.6889 (m-80) cc_final: 0.6674 (m-80) REVERT: B 13 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: E 112 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8474 (mtt180) REVERT: E 299 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7265 (ptm-80) REVERT: E 316 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: I 108 GLN cc_start: 0.8281 (pt0) cc_final: 0.7991 (pp30) REVERT: I 112 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8479 (mtt180) REVERT: I 299 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7505 (ptm-80) REVERT: I 316 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: I 399 ASN cc_start: 0.7719 (p0) cc_final: 0.7490 (p0) REVERT: F 13 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8340 (tt0) outliers start: 59 outliers final: 39 residues processed: 273 average time/residue: 0.7643 time to fit residues: 233.5465 Evaluate side-chains 267 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 274 LEU 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 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS 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 316 GLU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 404 GLN I 168 ASN I 404 GLN J 187 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.097386 restraints weight = 24487.166| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.21 r_work: 0.3005 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1660 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= 0.132 Angle : 0.584 8.372 31293 Z= 0.301 Chirality : 0.045 0.249 3207 Planarity : 0.004 0.040 3732 Dihedral : 19.264 179.979 4157 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.31 % Favored : 94.57 % Rotamer: Outliers : 2.47 % Allowed : 17.01 % Favored : 80.52 % 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: 1.22 (0.15), residues: 1209 sheet: 0.72 (0.28), residues: 351 loop : -0.21 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.021 0.001 TYR C 184 PHE 0.016 0.001 PHE B 31 TRP 0.014 0.001 TRP J 152 HIS 0.004 0.001 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00280 (23127) covalent geometry : angle 0.58379 (31293) hydrogen bonds : bond 0.04728 ( 1116) hydrogen bonds : angle 5.12525 ( 3276) *********************** 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 288 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 0.837 Fit side-chains REVERT: A 112 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8451 (mtt180) REVERT: A 299 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7422 (ptm-80) REVERT: A 316 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: C 235 PHE cc_start: 0.6817 (m-80) cc_final: 0.6612 (m-80) REVERT: B 13 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: B 245 GLN cc_start: 0.8531 (mm-40) cc_final: 0.7999 (mm110) REVERT: E 112 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8468 (mtt180) REVERT: E 299 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7364 (ptm-80) REVERT: E 316 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: I 108 GLN cc_start: 0.8275 (pt0) cc_final: 0.7971 (pp30) REVERT: I 112 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8484 (mtt180) REVERT: I 299 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7551 (ptm-80) REVERT: I 316 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: I 399 ASN cc_start: 0.7698 (p0) cc_final: 0.7497 (p0) REVERT: F 13 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: J 245 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8035 (mm110) outliers start: 54 outliers final: 35 residues processed: 276 average time/residue: 0.7809 time to fit residues: 240.8925 Evaluate side-chains 270 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 123 THR 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 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 207 SER 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 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 142 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 118 ASN G 118 ASN K 118 ASN E 404 GLN I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094849 restraints weight = 24507.112| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.21 r_work: 0.2947 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23127 Z= 0.191 Angle : 0.644 8.396 31293 Z= 0.336 Chirality : 0.047 0.261 3207 Planarity : 0.005 0.040 3732 Dihedral : 19.375 178.620 4157 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 2.42 % Allowed : 17.24 % Favored : 80.34 % 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: 0.86 (0.17), residues: 2559 helix: 1.18 (0.15), residues: 1221 sheet: 0.85 (0.28), residues: 339 loop : -0.19 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 115 TYR 0.023 0.002 TYR G 184 PHE 0.021 0.002 PHE G 248 TRP 0.016 0.002 TRP J 231 HIS 0.005 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00423 (23127) covalent geometry : angle 0.64356 (31293) hydrogen bonds : bond 0.05365 ( 1116) hydrogen bonds : angle 5.28567 ( 3276) ********************** 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 277 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 0.893 Fit side-chains REVERT: A 112 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8516 (mtt180) REVERT: A 299 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7479 (ptm-80) REVERT: A 316 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: C 45 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6723 (mt) REVERT: C 235 PHE cc_start: 0.6981 (m-80) cc_final: 0.6749 (m-80) REVERT: B 13 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: E 112 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8534 (mtt180) REVERT: E 299 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7351 (ptm-80) REVERT: E 316 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: I 108 GLN cc_start: 0.8387 (pt0) cc_final: 0.8073 (pp30) REVERT: I 112 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8558 (mtt180) REVERT: I 299 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7481 (ptm-80) REVERT: I 316 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: I 363 ASP cc_start: 0.8394 (m-30) cc_final: 0.7959 (m-30) REVERT: F 13 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8347 (tt0) outliers start: 53 outliers final: 36 residues processed: 270 average time/residue: 0.7785 time to fit residues: 234.8866 Evaluate side-chains 268 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 123 THR 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 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 207 SER 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 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 121 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 404 GLN I 168 ASN I 404 GLN J 187 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.096304 restraints weight = 24606.110| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.21 r_work: 0.2983 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1685 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= 0.144 Angle : 0.605 8.986 31293 Z= 0.313 Chirality : 0.046 0.254 3207 Planarity : 0.004 0.040 3732 Dihedral : 19.072 179.991 4157 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.08 % Favored : 94.80 % Rotamer: Outliers : 2.24 % Allowed : 17.51 % Favored : 80.25 % 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: 0.86 (0.17), residues: 2559 helix: 1.20 (0.15), residues: 1218 sheet: 0.86 (0.28), residues: 339 loop : -0.22 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 115 TYR 0.022 0.002 TYR G 184 PHE 0.017 0.001 PHE B 31 TRP 0.015 0.001 TRP B 231 HIS 0.004 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00311 (23127) covalent geometry : angle 0.60542 (31293) hydrogen bonds : bond 0.04923 ( 1116) hydrogen bonds : angle 5.20586 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8834.73 seconds wall clock time: 150 minutes 57.15 seconds (9057.15 seconds total)