Starting phenix.real_space_refine on Tue Jul 7 00:32:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s4i_24827/07_2026/7s4i_24827_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4i_24827/07_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_24827/07_2026/7s4i_24827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4i_24827/07_2026/7s4i_24827.map" model { file = "/net/cci-nas-00/data/ceres_data/7s4i_24827/07_2026/7s4i_24827_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4i_24827/07_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-6108/lib/python3.11/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, 10 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 314 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 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, 314 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Chain: "K" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 314 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 5.33, per 1000 atoms: 0.23 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: 1.99 Conformation dependent library (CDL) restraints added in 981.2 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: 0.58 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: 4.16 Time building geometry restraints manager: 2.56 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 3.060 nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 302 " model vdw 1.451 3.060 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.451 3.060 nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU E 501 " model vdw 1.967 3.060 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.968 3.060 ... (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: 0.04 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.740 Find NCS groups from input model: 0.510 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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/Z covalent geometry : bond 0.00841 / 0.44 (23127) covalent geometry : angle 1.01025 / 0.48 (31293) hydrogen bonds : bond 0.11523 / 7.42 ( 1116) hydrogen bonds : angle 6.17656 / 4.29 ( 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 : 0.879 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: 42 residues processed: 313 average time/residue: 0.7408 time to fit residues: 262.5261 Evaluate side-chains 276 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS 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 33 HIS 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 33 HIS 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: 0.3980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 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: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 HIS A 72 HIS C 118 ASN G 118 ASN K 118 ASN E 72 HIS E 168 ASN I 33 HIS I 72 HIS I 168 ASN F 187 ASN J 187 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.099139 restraints weight = 24033.701| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.20 r_work: 0.3029 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23127 Z= 0.145 Angle : 0.614 6.346 31293 Z= 0.315 Chirality : 0.046 0.330 3207 Planarity : 0.005 0.042 3732 Dihedral : 22.354 178.473 4217 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 3.29 % Allowed : 17.24 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2559 helix: 1.22 (0.15), residues: 1206 sheet: 0.75 (0.27), residues: 390 loop : -0.03 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 117 TYR 0.021 0.001 TYR C 184 PHE 0.016 0.002 PHE B 31 TRP 0.036 0.002 TRP G 234 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (23127) covalent geometry : angle 0.61405 / 0.32 (31293) hydrogen bonds : bond 0.04960 / 3.29 ( 1116) hydrogen bonds : angle 5.33126 / 3.75 ( 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 308 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 0.827 Fit side-chains REVERT: A 108 GLN cc_start: 0.8338 (pt0) cc_final: 0.7992 (pp30) REVERT: A 299 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7520 (ptm-80) REVERT: A 316 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: B 172 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7996 (tp30) REVERT: E 108 GLN cc_start: 0.8310 (pt0) cc_final: 0.8051 (pp30) REVERT: E 316 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: I 108 GLN cc_start: 0.8285 (pt0) cc_final: 0.7979 (pp30) REVERT: I 299 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7428 (ptm-80) REVERT: F 172 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8090 (tp30) REVERT: J 13 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8187 (tt0) outliers start: 72 outliers final: 26 residues processed: 295 average time/residue: 0.7446 time to fit residues: 248.5781 Evaluate side-chains 258 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR 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 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 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 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain I residue 46 THR 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: 0.0040 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN C 118 ASN ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 ASN K 118 ASN E 168 ASN 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 = 0.3453 r_free = 0.3453 target = 0.119142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.095138 restraints weight = 23776.572| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.16 r_work: 0.2952 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23127 Z= 0.206 Angle : 0.658 7.648 31293 Z= 0.345 Chirality : 0.048 0.292 3207 Planarity : 0.005 0.040 3732 Dihedral : 21.396 176.266 4164 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.31 % Favored : 94.57 % Rotamer: Outliers : 3.20 % Allowed : 16.32 % Favored : 80.48 % 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: 1.05 (0.15), residues: 1239 sheet: 0.86 (0.28), residues: 339 loop : -0.20 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.024 0.002 TYR G 184 PHE 0.021 0.002 PHE K 248 TRP 0.018 0.002 TRP J 231 HIS 0.006 0.002 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (23127) covalent geometry : angle 0.65828 / 0.35 (31293) hydrogen bonds : bond 0.05632 / 3.75 ( 1116) hydrogen bonds : angle 5.39649 / 3.79 ( 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 300 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 230 time to evaluate : 0.781 Fit side-chains REVERT: A 299 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7499 (ptm-80) REVERT: A 316 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: E 316 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: I 163 MET cc_start: 0.8833 (ttt) cc_final: 0.8570 (ttt) REVERT: I 299 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7518 (ptm-80) REVERT: I 316 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: F 13 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: J 13 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8222 (tt0) outliers start: 70 outliers final: 38 residues processed: 286 average time/residue: 0.7197 time to fit residues: 232.6011 Evaluate side-chains 266 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 397 THR 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 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 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 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 240 PHE 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 180 LEU 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 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 208 ARG 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 39 ILE 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: 9.9990 chunk 75 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 118 ASN G 118 ASN K 118 ASN E 33 HIS E 168 ASN I 168 ASN ** 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 = 0.3457 r_free = 0.3457 target = 0.119013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.094645 restraints weight = 23717.776| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.18 r_work: 0.2956 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1394 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 : 0.639 8.463 31293 Z= 0.333 Chirality : 0.047 0.277 3207 Planarity : 0.005 0.039 3732 Dihedral : 21.036 174.033 4163 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.92 % Favored : 94.96 % Rotamer: Outliers : 3.06 % Allowed : 17.01 % Favored : 79.93 % 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: 0.79 (0.17), residues: 2559 helix: 1.08 (0.15), residues: 1236 sheet: 0.86 (0.28), residues: 339 loop : -0.20 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 117 TYR 0.022 0.002 TYR G 184 PHE 0.019 0.002 PHE J 31 TRP 0.017 0.002 TRP J 231 HIS 0.005 0.001 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (23127) covalent geometry : angle 0.63936 / 0.33 (31293) hydrogen bonds : bond 0.05400 / 3.60 ( 1116) hydrogen bonds : angle 5.35141 / 3.76 ( 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 296 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 229 time to evaluate : 0.803 Fit side-chains REVERT: A 108 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8221 (pp30) REVERT: A 299 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7500 (ptm-80) REVERT: A 316 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: C 45 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6791 (mt) REVERT: G 45 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6718 (mt) REVERT: K 45 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6688 (mt) REVERT: E 108 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8080 (pp30) REVERT: E 299 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7366 (ptm-80) REVERT: E 316 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: I 108 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8074 (pp30) REVERT: I 163 MET cc_start: 0.8841 (ttt) cc_final: 0.8620 (ttt) REVERT: I 299 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7538 (ptm-80) REVERT: I 316 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: F 13 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: J 13 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8220 (tt0) outliers start: 67 outliers final: 29 residues processed: 279 average time/residue: 0.7471 time to fit residues: 234.8907 Evaluate side-chains 263 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 GLU 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 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 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 214 VAL Chi-restraints excluded: chain G residue 240 PHE 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 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU 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 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: 9.9990 chunk 85 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 HIS C 118 ASN G 118 ASN K 118 ASN I 168 ASN ** F 11 HIS ** 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 = 0.3447 r_free = 0.3447 target = 0.118837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.094595 restraints weight = 23304.401| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.16 r_work: 0.2943 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23127 Z= 0.202 Angle : 0.654 8.557 31293 Z= 0.342 Chirality : 0.048 0.279 3207 Planarity : 0.005 0.039 3732 Dihedral : 20.830 176.097 4157 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.28 % Favored : 94.61 % Rotamer: Outliers : 3.61 % Allowed : 16.14 % 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: 0.79 (0.17), residues: 2559 helix: 1.08 (0.15), residues: 1221 sheet: 0.85 (0.28), residues: 339 loop : -0.18 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 117 TYR 0.023 0.002 TYR G 184 PHE 0.020 0.002 PHE B 31 TRP 0.017 0.002 TRP J 231 HIS 0.006 0.002 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (23127) covalent geometry : angle 0.65395 / 0.34 (31293) hydrogen bonds : bond 0.05553 / 3.70 ( 1116) hydrogen bonds : angle 5.37481 / 3.78 ( 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 308 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 229 time to evaluate : 0.895 Fit side-chains REVERT: A 112 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8504 (mtt180) REVERT: A 299 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7464 (ptm-80) REVERT: A 316 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: K 45 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6703 (mt) REVERT: E 108 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8105 (pp30) REVERT: E 112 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8552 (mtt180) REVERT: E 299 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7333 (ptm-80) REVERT: E 316 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: I 112 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8543 (mtt180) REVERT: I 299 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7509 (ptm-80) REVERT: I 316 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: F 13 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8431 (tt0) outliers start: 79 outliers final: 37 residues processed: 288 average time/residue: 0.7602 time to fit residues: 246.9656 Evaluate side-chains 270 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 403 VAL Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER 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 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 214 VAL Chi-restraints excluded: chain G residue 240 PHE 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 K residue 274 LEU 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 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 208 ARG Chi-restraints excluded: chain I residue 227 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 153 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN G 118 ASN K 118 ASN E 168 ASN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.094199 restraints weight = 23545.138| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.17 r_work: 0.2936 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 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= 0.210 Angle : 0.652 8.721 31293 Z= 0.342 Chirality : 0.048 0.272 3207 Planarity : 0.005 0.039 3732 Dihedral : 20.709 175.489 4157 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.88 % Favored : 95.00 % Rotamer: Outliers : 3.52 % Allowed : 15.96 % 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: 0.78 (0.17), residues: 2559 helix: 1.07 (0.15), residues: 1224 sheet: 0.83 (0.28), residues: 339 loop : -0.16 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 115 TYR 0.022 0.002 TYR G 184 PHE 0.020 0.002 PHE G 248 TRP 0.017 0.002 TRP J 231 HIS 0.006 0.002 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (23127) covalent geometry : angle 0.65177 / 0.34 (31293) hydrogen bonds : bond 0.05569 / 3.71 ( 1116) hydrogen bonds : angle 5.38225 / 3.78 ( 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 301 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 224 time to evaluate : 0.864 Fit side-chains REVERT: A 112 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8484 (mtt180) REVERT: A 299 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7451 (ptm-80) REVERT: A 316 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: C 45 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6779 (mt) REVERT: K 45 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6702 (mt) REVERT: E 108 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8114 (pp30) REVERT: E 112 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8516 (mtt180) REVERT: E 316 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: I 112 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8523 (mtt180) REVERT: I 299 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7499 (ptm-80) REVERT: I 316 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: F 13 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8399 (tt0) outliers start: 77 outliers final: 40 residues processed: 280 average time/residue: 0.7746 time to fit residues: 243.9933 Evaluate side-chains 272 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 176 GLN 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 172 SER 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 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 240 PHE 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 K residue 274 LEU 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 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 208 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 250 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 48 HIS E 168 ASN I 48 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN F 187 ASN J 187 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.096335 restraints weight = 23233.665| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.16 r_work: 0.2977 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.1600 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= 0.152 Angle : 0.602 7.958 31293 Z= 0.314 Chirality : 0.046 0.259 3207 Planarity : 0.004 0.040 3732 Dihedral : 20.201 177.719 4157 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % Rotamer: Outliers : 2.83 % Allowed : 16.42 % Favored : 80.75 % 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: 0.87 (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 K 115 TYR 0.021 0.002 TYR C 184 PHE 0.018 0.002 PHE B 31 TRP 0.016 0.002 TRP I 206 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (23127) covalent geometry : angle 0.60238 / 0.31 (31293) hydrogen bonds : bond 0.05050 / 3.37 ( 1116) hydrogen bonds : angle 5.25136 / 3.69 ( 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 295 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 0.885 Fit side-chains REVERT: A 112 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8440 (mtt180) REVERT: A 299 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7460 (ptm-80) REVERT: A 316 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: E 108 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8040 (pp30) REVERT: E 112 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8478 (mtt180) REVERT: E 299 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7264 (ptm-80) REVERT: E 316 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: I 112 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8479 (mtt180) REVERT: I 299 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7506 (ptm-80) REVERT: I 316 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: I 399 ASN cc_start: 0.7716 (p0) cc_final: 0.7498 (p0) REVERT: F 13 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8367 (tt0) outliers start: 62 outliers final: 38 residues processed: 282 average time/residue: 0.7812 time to fit residues: 248.1084 Evaluate side-chains 272 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 B residue 8 VAL 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 113 LYS 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 123 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 274 LEU 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 316 GLU 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 208 ARG Chi-restraints excluded: chain I residue 227 LEU 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 Chi-restraints excluded: chain J residue 124 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: 1.9990 chunk 233 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN C 118 ASN B 187 ASN G 118 ASN K 118 ASN I 48 HIS I 72 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 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 = 0.3468 r_free = 0.3468 target = 0.119846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096291 restraints weight = 23173.412| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.14 r_work: 0.2981 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.1622 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= 0.154 Angle : 0.606 8.042 31293 Z= 0.316 Chirality : 0.046 0.256 3207 Planarity : 0.004 0.040 3732 Dihedral : 19.814 178.251 4157 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.16 % Favored : 94.72 % Rotamer: Outliers : 2.74 % Allowed : 16.55 % Favored : 80.70 % 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: 0.86 (0.17), residues: 2559 helix: 1.18 (0.15), residues: 1218 sheet: 0.88 (0.28), residues: 339 loop : -0.18 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 115 TYR 0.022 0.002 TYR C 184 PHE 0.018 0.002 PHE B 31 TRP 0.015 0.002 TRP J 231 HIS 0.005 0.001 HIS I 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (23127) covalent geometry : angle 0.60601 / 0.32 (31293) hydrogen bonds : bond 0.05052 / 3.37 ( 1116) hydrogen bonds : angle 5.22925 / 3.68 ( 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 293 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 0.760 Fit side-chains REVERT: A 112 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8458 (mtt180) REVERT: A 299 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7466 (ptm-80) REVERT: A 316 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: E 108 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8085 (pp30) REVERT: E 112 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8486 (mtt180) REVERT: E 299 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7269 (ptm-80) REVERT: E 316 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: I 112 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8497 (mtt180) REVERT: I 299 ARG cc_start: 0.7877 (ttp80) cc_final: 0.7406 (ptm-80) REVERT: I 316 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: I 363 ASP cc_start: 0.8385 (m-30) cc_final: 0.8173 (m-30) REVERT: I 399 ASN cc_start: 0.7719 (p0) cc_final: 0.7503 (p0) REVERT: F 13 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8325 (tt0) outliers start: 60 outliers final: 38 residues processed: 277 average time/residue: 0.7934 time to fit residues: 246.9516 Evaluate side-chains 267 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 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 207 SER Chi-restraints excluded: chain G residue 214 VAL 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 316 GLU 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 208 ARG 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 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 Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 118 ASN G 118 ASN K 118 ASN E 48 HIS E 72 HIS E 168 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN I 404 GLN 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 = 0.3451 r_free = 0.3451 target = 0.118747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.095179 restraints weight = 23364.617| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.14 r_work: 0.2959 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23127 Z= 0.184 Angle : 0.635 8.366 31293 Z= 0.331 Chirality : 0.047 0.260 3207 Planarity : 0.005 0.040 3732 Dihedral : 19.736 177.299 4156 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 2.70 % Allowed : 16.78 % 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: 0.81 (0.17), residues: 2559 helix: 1.14 (0.15), residues: 1221 sheet: 0.84 (0.28), residues: 339 loop : -0.21 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 115 TYR 0.023 0.002 TYR C 184 PHE 0.020 0.002 PHE K 248 TRP 0.016 0.002 TRP J 231 HIS 0.005 0.001 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (23127) covalent geometry : angle 0.63537 / 0.33 (31293) hydrogen bonds : bond 0.05314 / 3.55 ( 1116) hydrogen bonds : angle 5.29481 / 3.72 ( 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 279 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 220 time to evaluate : 0.883 Fit side-chains REVERT: A 112 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8486 (mtt180) REVERT: A 299 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7452 (ptm-80) REVERT: A 316 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: E 108 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8061 (pp30) REVERT: E 112 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8508 (mtt180) REVERT: E 299 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7332 (ptm-80) REVERT: E 316 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: I 112 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8517 (mtt180) REVERT: I 299 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7472 (ptm-80) REVERT: I 316 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: I 399 ASN cc_start: 0.7719 (p0) cc_final: 0.7509 (p0) REVERT: F 13 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8322 (tt0) outliers start: 59 outliers final: 41 residues processed: 264 average time/residue: 0.8024 time to fit residues: 237.8091 Evaluate side-chains 268 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 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 113 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 207 SER 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 316 GLU 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 208 ARG 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 I residue 403 VAL Chi-restraints excluded: chain I residue 404 GLN 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: 3.9990 chunk 141 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 53 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 163 optimal weight: 0.1980 chunk 115 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 72 HIS I 168 ASN I 404 GLN F 187 ASN J 187 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.097150 restraints weight = 23159.528| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.17 r_work: 0.2998 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23127 Z= 0.136 Angle : 0.598 8.652 31293 Z= 0.309 Chirality : 0.045 0.253 3207 Planarity : 0.004 0.040 3732 Dihedral : 19.356 179.198 4156 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % Rotamer: Outliers : 2.10 % Allowed : 17.47 % Favored : 80.43 % 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: 1206 sheet: 0.88 (0.29), residues: 339 loop : -0.25 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 B 231 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (23127) covalent geometry : angle 0.59807 / 0.31 (31293) hydrogen bonds : bond 0.04831 / 3.22 ( 1116) hydrogen bonds : angle 5.20399 / 3.66 ( 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 270 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.875 Fit side-chains REVERT: A 112 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8422 (mtt180) REVERT: A 299 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7477 (ptm-80) REVERT: A 316 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: E 108 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8056 (pp30) REVERT: E 112 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8451 (mtt180) REVERT: E 299 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7333 (ptm-80) REVERT: I 112 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8448 (mtt180) REVERT: I 299 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7391 (ptm-80) REVERT: I 316 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: I 363 ASP cc_start: 0.8399 (m-30) cc_final: 0.8166 (m-30) REVERT: I 399 ASN cc_start: 0.7723 (p0) cc_final: 0.7518 (p0) REVERT: F 13 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8333 (tt0) outliers start: 46 outliers final: 34 residues processed: 259 average time/residue: 0.8320 time to fit residues: 241.0538 Evaluate side-chains 263 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 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 207 SER Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 207 SER 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 403 VAL Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 316 GLU 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: 0.9980 chunk 218 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 225 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 168 ASN I 168 ASN 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 = 0.3482 r_free = 0.3482 target = 0.120797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096688 restraints weight = 23295.305| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.17 r_work: 0.2992 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.1694 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= 0.147 Angle : 0.603 8.712 31293 Z= 0.312 Chirality : 0.046 0.254 3207 Planarity : 0.004 0.040 3732 Dihedral : 19.253 179.456 4156 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 2.01 % Allowed : 17.51 % Favored : 80.48 % 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: 1.21 (0.15), residues: 1206 sheet: 0.88 (0.29), residues: 339 loop : -0.25 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 115 TYR 0.022 0.002 TYR G 184 PHE 0.017 0.002 PHE B 31 TRP 0.015 0.001 TRP B 231 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (23127) covalent geometry : angle 0.60275 / 0.31 (31293) hydrogen bonds : bond 0.04933 / 3.30 ( 1116) hydrogen bonds : angle 5.20030 / 3.66 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9079.60 seconds wall clock time: 155 minutes 22.67 seconds (9322.67 seconds total)