Starting phenix.real_space_refine on Tue Jul 7 02:52:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqw_40714/07_2026/8sqw_40714_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqw_40714/07_2026/8sqw_40714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sqw_40714/07_2026/8sqw_40714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqw_40714/07_2026/8sqw_40714.map" model { file = "/net/cci-nas-00/data/ceres_data/8sqw_40714/07_2026/8sqw_40714_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqw_40714/07_2026/8sqw_40714_trim.cif" } resolution = 2.16 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= 0.001 sd= 0.006 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 20898 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: 7 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15036 2.51 5 N 3417 2.21 5 O 4250 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 22850 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: "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: "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: "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: "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: "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: "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: "C" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 320 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: "G" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 320 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 8} Chain breaks: 1 Chain: "K" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 320 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 8} Chain breaks: 1 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: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} 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: "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} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 4.69, per 1000 atoms: 0.21 Number of scatterers: 22850 At special positions: 0 Unit cell: (106.878, 108.995, 119.577, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 F 9 9.00 O 4250 8.00 N 3417 7.00 C 15036 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: 1.96 Conformation dependent library (CDL) restraints added in 876.2 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: 93 helices and 18 sheets defined 51.1% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 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: 3.672A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) 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: 3.763A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 73 removed outlier: 3.905A 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 155 Processing helix chain 'C' and resid 181 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: 4.453A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 245 through 254 removed outlier: 3.760A pdb=" N PHE C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.697A 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 '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: 3.631A 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: 3.630A 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: 3.958A 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: 4.109A 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: 3.764A 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: 3.672A 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: 3.957A 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: 4.109A 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 helix chain 'G' and resid 49 through 73 removed outlier: 3.905A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.623A 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 155 Processing helix chain 'G' and resid 181 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: 4.341A 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: 4.453A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 244 No H-bonds generated for 'chain 'G' and resid 242 through 244' Processing helix chain 'G' and resid 245 through 254 removed outlier: 3.760A pdb=" N PHE G 251 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.697A 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: 3.905A 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 155 Processing helix chain 'K' and resid 181 through 199 Processing helix chain 'K' and resid 207 through 233 Proline residue: K 217 - end of helix removed outlier: 3.578A 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: 4.662A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 242 through 244 No H-bonds generated for 'chain 'K' and resid 242 through 244' Processing helix chain 'K' and resid 245 through 254 removed outlier: 3.760A pdb=" N PHE K 251 " --> pdb=" O GLY K 247 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU K 254 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 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: 4.484A 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: 6.730A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.744A 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: 6.670A pdb=" N VAL A 144 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE A 151 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET A 142 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.829A 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: 3.920A 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: 6.694A 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: 7.258A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.331A 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: 6.554A 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: 6.448A 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: 4.295A 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: 6.731A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.685A 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: 5.203A pdb=" N ILE E 151 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET E 142 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.827A 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: 5.813A 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: 4.498A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 6.694A 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: 7.258A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.332A 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: 6.553A 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: 6.666A 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: 6.729A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.744A 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: 6.670A 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: 3.827A 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: 3.921A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 4.496A 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: 7.258A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.676A 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: 7.331A 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: 6.553A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.450A 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 1080 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.84 Time building geometry restraints manager: 2.50 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: 3368 1.32 - 1.44: 6755 1.44 - 1.57: 12701 1.57 - 1.69: 138 1.69 - 1.81: 180 Bond restraints: 23142 Sorted by residual: 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 4.00e+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 3.95e+01 bond pdb=" CB PLC K 303 " pdb=" O3 PLC K 303 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CB PLC G 301 " pdb=" O3 PLC G 301 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CB PLC C 311 " pdb=" O3 PLC C 311 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.94e+01 ... (remaining 23137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 29630 2.18 - 4.36: 1301 4.36 - 6.54: 251 6.54 - 8.72: 51 8.72 - 10.90: 81 Bond angle restraints: 31314 Sorted by residual: angle pdb=" C PHE G 248 " pdb=" N VAL G 249 " pdb=" CA VAL G 249 " ideal model delta sigma weight residual 120.56 109.66 10.90 1.28e+00 6.10e-01 7.25e+01 angle pdb=" C PHE K 248 " pdb=" N VAL K 249 " pdb=" CA VAL K 249 " ideal model delta sigma weight residual 120.56 109.67 10.89 1.28e+00 6.10e-01 7.24e+01 angle pdb=" C PHE C 248 " pdb=" N VAL C 249 " pdb=" CA VAL C 249 " ideal model delta sigma weight residual 120.56 109.68 10.88 1.28e+00 6.10e-01 7.23e+01 angle pdb=" N PHE G 248 " pdb=" CA PHE G 248 " pdb=" C PHE G 248 " ideal model delta sigma weight residual 112.23 102.93 9.30 1.26e+00 6.30e-01 5.45e+01 angle pdb=" N PHE C 248 " pdb=" CA PHE C 248 " pdb=" C PHE C 248 " ideal model delta sigma weight residual 112.23 102.95 9.28 1.26e+00 6.30e-01 5.42e+01 ... (remaining 31309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 12593 34.44 - 68.89: 808 68.89 - 103.33: 99 103.33 - 137.77: 36 137.77 - 172.21: 12 Dihedral angle restraints: 13548 sinusoidal: 6096 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 -55.71 116.50 -172.21 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 -55.71 116.49 -172.20 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC C 311 " pdb=" C1 PLC C 311 " pdb=" C2 PLC C 311 " pdb=" O3P PLC C 311 " ideal model delta sinusoidal sigma weight residual -55.71 116.47 -172.18 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2378 0.052 - 0.104: 639 0.104 - 0.155: 129 0.155 - 0.207: 46 0.207 - 0.259: 15 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA TYR K 246 " pdb=" N TYR K 246 " pdb=" C TYR K 246 " pdb=" CB TYR K 246 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TYR G 246 " pdb=" N TYR G 246 " pdb=" C TYR G 246 " pdb=" CB TYR G 246 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TYR C 246 " pdb=" N TYR C 246 " pdb=" C TYR C 246 " pdb=" CB TYR C 246 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 165 " 0.634 9.50e-02 1.11e+02 2.84e-01 4.97e+01 pdb=" NE ARG G 165 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG G 165 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG G 165 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 165 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 165 " -0.634 9.50e-02 1.11e+02 2.84e-01 4.97e+01 pdb=" NE ARG K 165 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG K 165 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG K 165 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 165 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 165 " -0.634 9.50e-02 1.11e+02 2.84e-01 4.97e+01 pdb=" NE ARG C 165 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG C 165 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 165 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 165 " -0.019 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 54 2.29 - 2.95: 10794 2.95 - 3.60: 36195 3.60 - 4.25: 63649 4.25 - 4.90: 102638 Nonbonded interactions: 213330 Sorted by model distance: nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 302 " model vdw 1.642 3.060 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.643 3.060 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.643 3.060 nonbonded pdb=" F2 ETF C 310 " pdb=" O HOH C 402 " model vdw 1.861 2.990 nonbonded pdb=" F2 ETF C 310 " pdb=" O HOH C 401 " model vdw 1.875 2.990 ... (remaining 213325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 304 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: 0.000 Normalize map: mean=0, sd=1: 12.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.310 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.126 23142 Z= 0.484 Angle : 1.087 10.896 31314 Z= 0.560 Chirality : 0.054 0.259 3207 Planarity : 0.009 0.284 3732 Dihedral : 22.730 172.214 8790 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.10 % Favored : 93.32 % Rotamer: Outliers : 4.12 % Allowed : 17.70 % Favored : 78.19 % Cbeta Deviations : 0.04 % 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: 0.57 (0.17), residues: 2559 helix: 1.05 (0.16), residues: 1182 sheet: 1.30 (0.28), residues: 357 loop : -0.71 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 165 TYR 0.040 0.002 TYR G 178 PHE 0.020 0.002 PHE K 240 TRP 0.017 0.002 TRP E 202 HIS 0.049 0.004 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00883 / 0.48 (23142) covalent geometry : angle 1.08657 / 0.56 (31314) hydrogen bonds : bond 0.11580 / 7.70 ( 1080) hydrogen bonds : angle 6.51796 / 4.61 ( 3168) *********************** 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 500 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 410 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: K 165 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7194 (mtt90) outliers start: 90 outliers final: 30 residues processed: 486 average time/residue: 0.6353 time to fit residues: 351.9100 Evaluate side-chains 304 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 309 ASN Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR 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 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 231 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN E 38 GLN E 404 GLN I 38 GLN K 91 ASN K 276 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.148747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124745 restraints weight = 31652.354| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.20 r_work: 0.3551 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23142 Z= 0.181 Angle : 0.708 9.997 31314 Z= 0.358 Chirality : 0.048 0.334 3207 Planarity : 0.005 0.041 3732 Dihedral : 22.287 179.173 4211 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 4.44 % Allowed : 17.88 % Favored : 77.69 % 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: 0.53 (0.17), residues: 2559 helix: 0.92 (0.15), residues: 1206 sheet: 0.95 (0.28), residues: 369 loop : -0.50 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 165 TYR 0.022 0.002 TYR C 184 PHE 0.021 0.002 PHE J 31 TRP 0.040 0.002 TRP K 234 HIS 0.007 0.002 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (23142) covalent geometry : angle 0.70759 / 0.36 (31314) hydrogen bonds : bond 0.05060 / 3.42 ( 1080) hydrogen bonds : angle 5.41922 / 3.87 ( 3168) *********************** 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 420 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 323 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7139 (mp) REVERT: B 11 HIS cc_start: 0.7885 (m-70) cc_final: 0.7617 (m-70) REVERT: C 235 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6785 (t80) REVERT: E 404 GLN cc_start: 0.7708 (tt0) cc_final: 0.7463 (tt0) REVERT: I 227 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.6867 (mp) REVERT: F 11 HIS cc_start: 0.7826 (m-70) cc_final: 0.7519 (m-70) REVERT: J 11 HIS cc_start: 0.7905 (m-70) cc_final: 0.7485 (m-70) REVERT: G 130 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7739 (mtt90) REVERT: K 130 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7476 (mtt90) REVERT: K 156 ASP cc_start: 0.7257 (m-30) cc_final: 0.7022 (m-30) REVERT: K 235 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6815 (t80) outliers start: 97 outliers final: 37 residues processed: 389 average time/residue: 0.5969 time to fit residues: 265.9868 Evaluate side-chains 318 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN 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 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 235 PHE Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J 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 130 ARG Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 235 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN K 91 ASN K 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.144488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120470 restraints weight = 31484.482| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.17 r_work: 0.3482 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 23142 Z= 0.342 Angle : 0.798 9.822 31314 Z= 0.414 Chirality : 0.052 0.262 3207 Planarity : 0.006 0.056 3732 Dihedral : 21.488 179.159 4180 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 4.76 % Allowed : 16.83 % Favored : 78.42 % 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: 0.40 (0.17), residues: 2559 helix: 0.89 (0.15), residues: 1200 sheet: 0.62 (0.28), residues: 339 loop : -0.51 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 208 TYR 0.029 0.003 TYR C 184 PHE 0.025 0.003 PHE F 31 TRP 0.025 0.003 TRP J 231 HIS 0.009 0.003 HIS I 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.34 (23142) covalent geometry : angle 0.79770 / 0.41 (31314) hydrogen bonds : bond 0.06002 / 4.05 ( 1080) hydrogen bonds : angle 5.69191 / 4.06 ( 3168) *********************** 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 398 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 294 time to evaluate : 0.603 Fit side-chains REVERT: A 145 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: B 11 HIS cc_start: 0.7671 (m-70) cc_final: 0.7420 (m-70) REVERT: C 130 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7861 (mtp180) REVERT: C 235 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6988 (t80) REVERT: I 163 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8054 (ttt) REVERT: I 167 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6966 (mmp80) REVERT: I 227 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7347 (mp) REVERT: F 11 HIS cc_start: 0.7771 (m-70) cc_final: 0.7498 (m-70) REVERT: J 11 HIS cc_start: 0.7726 (m-70) cc_final: 0.7469 (m-70) REVERT: J 241 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: G 130 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7809 (mtt90) REVERT: G 235 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.7143 (t80) REVERT: K 130 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7916 (mtt180) REVERT: K 235 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6960 (t80) outliers start: 104 outliers final: 48 residues processed: 362 average time/residue: 0.5821 time to fit residues: 241.2911 Evaluate side-chains 326 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 267 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 288 ASP 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 C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 163 MET Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 ILE 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 29 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 235 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 120 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 221 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN B 174 ASN B 187 ASN E 72 HIS ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 404 GLN F 174 ASN J 174 ASN G 91 ASN G 155 GLN K 91 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.147494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124107 restraints weight = 30656.723| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.15 r_work: 0.3533 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23142 Z= 0.163 Angle : 0.652 8.883 31314 Z= 0.335 Chirality : 0.046 0.236 3207 Planarity : 0.005 0.040 3732 Dihedral : 20.666 172.216 4170 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.92 % Rotamer: Outliers : 4.48 % Allowed : 17.38 % Favored : 78.14 % 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: 0.52 (0.17), residues: 2559 helix: 1.05 (0.15), residues: 1197 sheet: 0.55 (0.29), residues: 339 loop : -0.49 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 129 TYR 0.022 0.002 TYR G 184 PHE 0.017 0.002 PHE F 31 TRP 0.018 0.002 TRP B 231 HIS 0.007 0.001 HIS K 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (23142) covalent geometry : angle 0.65217 / 0.34 (31314) hydrogen bonds : bond 0.04935 / 3.35 ( 1080) hydrogen bonds : angle 5.42729 / 3.87 ( 3168) *********************** 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 383 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 285 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 227 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7292 (mp) REVERT: A 339 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7452 (p0) REVERT: B 11 HIS cc_start: 0.7841 (m-70) cc_final: 0.7559 (m-70) REVERT: B 198 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8070 (ttp80) REVERT: C 130 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7872 (mtp180) REVERT: C 235 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6401 (t80) REVERT: I 227 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7325 (mp) REVERT: I 404 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: F 11 HIS cc_start: 0.7854 (m-70) cc_final: 0.7557 (m-70) REVERT: J 11 HIS cc_start: 0.7837 (m-70) cc_final: 0.7563 (m-70) REVERT: G 129 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7961 (mtt90) REVERT: G 130 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7881 (mtt90) REVERT: G 235 PHE cc_start: 0.7151 (t80) cc_final: 0.6854 (t80) REVERT: K 235 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6602 (t80) outliers start: 98 outliers final: 41 residues processed: 352 average time/residue: 0.5789 time to fit residues: 232.8730 Evaluate side-chains 316 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 ASP 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 198 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain I residue 414 MET 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 J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 235 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 126 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 404 GLN B 187 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN G 155 GLN K 91 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.147445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123766 restraints weight = 30613.678| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.17 r_work: 0.3525 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23142 Z= 0.174 Angle : 0.653 8.696 31314 Z= 0.336 Chirality : 0.046 0.214 3207 Planarity : 0.005 0.041 3732 Dihedral : 20.008 167.532 4170 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 4.30 % Allowed : 17.51 % Favored : 78.19 % 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: 0.62 (0.17), residues: 2559 helix: 1.13 (0.15), residues: 1191 sheet: 0.55 (0.29), residues: 339 loop : -0.40 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 129 TYR 0.023 0.002 TYR C 184 PHE 0.017 0.002 PHE J 31 TRP 0.018 0.002 TRP B 231 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (23142) covalent geometry : angle 0.65341 / 0.34 (31314) hydrogen bonds : bond 0.04935 / 3.34 ( 1080) hydrogen bonds : angle 5.38295 / 3.84 ( 3168) *********************** 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 368 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 274 time to evaluate : 0.679 Fit side-chains REVERT: A 218 MET cc_start: 0.8353 (mmm) cc_final: 0.8101 (mmm) REVERT: A 227 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7317 (mp) REVERT: A 339 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7431 (p0) REVERT: B 11 HIS cc_start: 0.7827 (m-70) cc_final: 0.7612 (m-70) REVERT: C 130 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7845 (mtp180) REVERT: C 235 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6552 (t80) REVERT: E 45 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.6703 (mtp85) REVERT: E 145 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: I 145 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: I 227 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7167 (mp) REVERT: F 11 HIS cc_start: 0.7868 (m-70) cc_final: 0.7583 (m-70) REVERT: J 11 HIS cc_start: 0.7855 (m-70) cc_final: 0.7541 (m-70) REVERT: G 235 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6819 (t80) REVERT: K 235 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6615 (t80) outliers start: 94 outliers final: 47 residues processed: 340 average time/residue: 0.5876 time to fit residues: 229.2609 Evaluate side-chains 318 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET 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 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 130 ARG Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 288 ASP 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 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL 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 235 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 235 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 130 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN E 72 HIS ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN K 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.144208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119891 restraints weight = 31878.885| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.19 r_work: 0.3457 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 23142 Z= 0.371 Angle : 0.809 10.275 31314 Z= 0.421 Chirality : 0.051 0.228 3207 Planarity : 0.006 0.080 3732 Dihedral : 19.831 164.518 4170 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.20 % Favored : 94.65 % Rotamer: Outliers : 4.85 % Allowed : 16.83 % Favored : 78.33 % 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: 0.47 (0.17), residues: 2559 helix: 0.95 (0.15), residues: 1197 sheet: 0.48 (0.28), residues: 339 loop : -0.39 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 208 TYR 0.028 0.003 TYR C 184 PHE 0.023 0.003 PHE J 31 TRP 0.025 0.003 TRP J 231 HIS 0.009 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00820 / 0.37 (23142) covalent geometry : angle 0.80897 / 0.42 (31314) hydrogen bonds : bond 0.06031 / 4.07 ( 1080) hydrogen bonds : angle 5.71933 / 4.07 ( 3168) *********************** 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 378 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 272 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: A 339 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7612 (p0) REVERT: B 11 HIS cc_start: 0.7858 (m-70) cc_final: 0.7601 (m-70) REVERT: B 198 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8188 (ttp80) REVERT: C 129 ARG cc_start: 0.8244 (mtt90) cc_final: 0.7991 (mtt90) REVERT: C 130 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7858 (mtp180) REVERT: C 235 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6967 (t80) REVERT: E 145 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: I 145 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: I 227 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7337 (mp) REVERT: F 11 HIS cc_start: 0.7883 (m-70) cc_final: 0.7590 (m-70) REVERT: F 241 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: J 11 HIS cc_start: 0.7864 (m-70) cc_final: 0.7515 (m-70) REVERT: J 241 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: G 129 ARG cc_start: 0.8290 (mtt90) cc_final: 0.8065 (mtt90) REVERT: G 130 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7948 (mtp85) REVERT: G 235 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.7135 (t80) REVERT: K 130 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7841 (mtt90) REVERT: K 235 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6841 (t80) outliers start: 106 outliers final: 51 residues processed: 345 average time/residue: 0.6354 time to fit residues: 249.7102 Evaluate side-chains 323 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 258 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 79 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 198 ARG 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 130 ARG Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP 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 33 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 245 GLN 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 130 ARG Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 235 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 15 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 185 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN B 187 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN K 91 ASN K 276 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.148132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124929 restraints weight = 31119.332| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.17 r_work: 0.3531 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23142 Z= 0.146 Angle : 0.648 9.860 31314 Z= 0.332 Chirality : 0.045 0.197 3207 Planarity : 0.005 0.056 3732 Dihedral : 19.038 159.003 4170 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.92 % Favored : 94.96 % Rotamer: Outliers : 3.57 % Allowed : 18.43 % Favored : 78.01 % 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: 0.55 (0.17), residues: 2559 helix: 1.08 (0.15), residues: 1197 sheet: 0.48 (0.28), residues: 339 loop : -0.43 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 208 TYR 0.021 0.001 TYR K 184 PHE 0.015 0.001 PHE B 31 TRP 0.018 0.002 TRP E 202 HIS 0.007 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (23142) covalent geometry : angle 0.64769 / 0.33 (31314) hydrogen bonds : bond 0.04704 / 3.19 ( 1080) hydrogen bonds : angle 5.38268 / 3.84 ( 3168) *********************** 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 364 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 286 time to evaluate : 0.737 Fit side-chains REVERT: A 233 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7631 (mtp85) REVERT: A 339 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7526 (p0) REVERT: B 11 HIS cc_start: 0.7982 (m-70) cc_final: 0.7716 (m-70) REVERT: C 129 ARG cc_start: 0.8261 (mtt90) cc_final: 0.7940 (mtt90) REVERT: C 130 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7889 (mtp180) REVERT: C 235 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6689 (t80) REVERT: I 218 MET cc_start: 0.8393 (mmm) cc_final: 0.8159 (mmm) REVERT: I 227 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7318 (mp) REVERT: I 233 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7732 (mtp85) REVERT: F 11 HIS cc_start: 0.7940 (m-70) cc_final: 0.7641 (m-70) REVERT: J 11 HIS cc_start: 0.7911 (m-70) cc_final: 0.7591 (m-70) REVERT: G 129 ARG cc_start: 0.8296 (mtt90) cc_final: 0.7979 (mtt90) REVERT: G 235 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6752 (t80) REVERT: K 129 ARG cc_start: 0.8256 (mtt90) cc_final: 0.7928 (mtt90) REVERT: K 235 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6583 (t80) outliers start: 78 outliers final: 36 residues processed: 345 average time/residue: 0.5764 time to fit residues: 228.1967 Evaluate side-chains 306 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 235 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 190 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 404 GLN B 187 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN K 91 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.144639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120561 restraints weight = 31538.623| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.23 r_work: 0.3460 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 23142 Z= 0.267 Angle : 0.727 9.568 31314 Z= 0.378 Chirality : 0.049 0.208 3207 Planarity : 0.005 0.047 3732 Dihedral : 18.764 156.824 4164 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 3.16 % Allowed : 19.71 % Favored : 77.14 % 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: 0.54 (0.17), residues: 2559 helix: 1.11 (0.15), residues: 1182 sheet: 0.42 (0.28), residues: 339 loop : -0.44 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 208 TYR 0.025 0.002 TYR C 184 PHE 0.021 0.002 PHE K 248 TRP 0.022 0.002 TRP J 231 HIS 0.007 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.27 (23142) covalent geometry : angle 0.72742 / 0.38 (31314) hydrogen bonds : bond 0.05474 / 3.70 ( 1080) hydrogen bonds : angle 5.52739 / 3.94 ( 3168) *********************** 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 341 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 272 time to evaluate : 0.655 Fit side-chains REVERT: A 145 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: A 218 MET cc_start: 0.8489 (mmm) cc_final: 0.8241 (mmm) REVERT: A 339 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7544 (p0) REVERT: B 11 HIS cc_start: 0.7906 (m-70) cc_final: 0.7666 (m-70) REVERT: C 129 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7983 (mtt90) REVERT: C 130 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7911 (mtp180) REVERT: C 235 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6706 (t80) REVERT: E 145 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: E 233 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7524 (mtm180) REVERT: I 218 MET cc_start: 0.8435 (mmm) cc_final: 0.8227 (mmm) REVERT: I 227 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7377 (mp) REVERT: I 233 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7758 (mtp85) REVERT: F 11 HIS cc_start: 0.7938 (m-70) cc_final: 0.7676 (m-70) REVERT: J 11 HIS cc_start: 0.7904 (m-70) cc_final: 0.7604 (m-70) REVERT: G 129 ARG cc_start: 0.8300 (mtt90) cc_final: 0.7983 (mtt90) REVERT: G 235 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6986 (t80) REVERT: K 129 ARG cc_start: 0.8193 (mtt90) cc_final: 0.7900 (mtt90) REVERT: K 235 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6742 (t80) outliers start: 69 outliers final: 43 residues processed: 324 average time/residue: 0.5758 time to fit residues: 213.9657 Evaluate side-chains 315 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU 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 130 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 235 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 226 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN B 187 ASN C 276 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN J 187 ASN G 91 ASN K 91 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.147502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123588 restraints weight = 31392.642| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.29 r_work: 0.3515 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23142 Z= 0.147 Angle : 0.652 8.950 31314 Z= 0.335 Chirality : 0.045 0.176 3207 Planarity : 0.004 0.044 3732 Dihedral : 18.228 153.869 4164 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.92 % Rotamer: Outliers : 2.97 % Allowed : 19.89 % Favored : 77.14 % 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: 0.62 (0.17), residues: 2559 helix: 1.15 (0.15), residues: 1203 sheet: 0.49 (0.29), residues: 339 loop : -0.43 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 208 TYR 0.021 0.001 TYR C 184 PHE 0.014 0.001 PHE J 31 TRP 0.017 0.002 TRP E 202 HIS 0.004 0.001 HIS K 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (23142) covalent geometry : angle 0.65210 / 0.34 (31314) hydrogen bonds : bond 0.04688 / 3.18 ( 1080) hydrogen bonds : angle 5.33872 / 3.81 ( 3168) *********************** 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 338 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 273 time to evaluate : 0.764 Fit side-chains REVERT: A 218 MET cc_start: 0.8447 (mmm) cc_final: 0.8164 (mmm) REVERT: A 227 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7399 (mp) REVERT: A 339 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7511 (p0) REVERT: B 11 HIS cc_start: 0.8030 (m-70) cc_final: 0.7603 (m90) REVERT: C 129 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8024 (mtt90) REVERT: C 130 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7942 (mtp180) REVERT: E 233 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7610 (mtp85) REVERT: I 45 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6638 (mtp85) REVERT: I 218 MET cc_start: 0.8393 (mmm) cc_final: 0.8180 (mmm) REVERT: I 227 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7248 (mp) REVERT: I 233 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7719 (mtp85) REVERT: F 11 HIS cc_start: 0.8034 (m-70) cc_final: 0.7766 (m-70) REVERT: J 11 HIS cc_start: 0.7968 (m-70) cc_final: 0.7689 (m-70) REVERT: G 129 ARG cc_start: 0.8390 (mtt90) cc_final: 0.8050 (mtt90) REVERT: G 235 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6744 (t80) REVERT: K 129 ARG cc_start: 0.8279 (mtt90) cc_final: 0.7895 (mtt90) REVERT: K 235 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6567 (t80) outliers start: 65 outliers final: 40 residues processed: 322 average time/residue: 0.5762 time to fit residues: 212.9816 Evaluate side-chains 313 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 235 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 189 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 145 optimal weight: 0.0050 chunk 69 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 254 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN B 187 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN F 187 ASN J 187 ASN G 91 ASN K 91 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125520 restraints weight = 31512.366| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.20 r_work: 0.3557 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23142 Z= 0.138 Angle : 0.637 9.701 31314 Z= 0.325 Chirality : 0.045 0.171 3207 Planarity : 0.004 0.044 3732 Dihedral : 17.670 150.910 4164 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 2.51 % Allowed : 20.53 % Favored : 76.95 % 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: 0.69 (0.17), residues: 2559 helix: 1.25 (0.15), residues: 1188 sheet: 0.56 (0.29), residues: 339 loop : -0.43 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 208 TYR 0.021 0.001 TYR G 184 PHE 0.017 0.001 PHE K 248 TRP 0.021 0.002 TRP B 237 HIS 0.003 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (23142) covalent geometry : angle 0.63691 / 0.33 (31314) hydrogen bonds : bond 0.04474 / 3.04 ( 1080) hydrogen bonds : angle 5.22196 / 3.72 ( 3168) ********************** 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 333 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 278 time to evaluate : 0.881 Fit side-chains REVERT: A 218 MET cc_start: 0.8381 (mmm) cc_final: 0.8116 (mmm) REVERT: A 227 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7306 (mp) REVERT: B 11 HIS cc_start: 0.7999 (m-70) cc_final: 0.7646 (m90) REVERT: C 86 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7458 (tm-30) REVERT: C 129 ARG cc_start: 0.8305 (mtt90) cc_final: 0.7990 (mtt90) REVERT: C 235 PHE cc_start: 0.7141 (t80) cc_final: 0.6900 (t80) REVERT: E 233 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7529 (mtp85) REVERT: I 227 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7113 (mp) REVERT: I 233 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7757 (mtp85) REVERT: F 11 HIS cc_start: 0.7961 (m-70) cc_final: 0.7574 (m90) REVERT: J 11 HIS cc_start: 0.7909 (m-70) cc_final: 0.7708 (m-70) REVERT: G 129 ARG cc_start: 0.8265 (mtt90) cc_final: 0.8013 (mtt90) REVERT: G 235 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6760 (t80) REVERT: K 129 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7811 (mtt90) REVERT: K 235 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6585 (t80) outliers start: 55 outliers final: 34 residues processed: 319 average time/residue: 0.5956 time to fit residues: 217.8709 Evaluate side-chains 301 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 235 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 130 optimal weight: 0.0970 chunk 221 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN G 91 ASN K 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.145234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.121638 restraints weight = 31440.689| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.18 r_work: 0.3498 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23142 Z= 0.242 Angle : 0.725 9.720 31314 Z= 0.375 Chirality : 0.048 0.196 3207 Planarity : 0.005 0.045 3732 Dihedral : 17.807 150.221 4160 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 2.42 % Allowed : 21.08 % Favored : 76.50 % 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: 0.68 (0.17), residues: 2559 helix: 1.25 (0.15), residues: 1182 sheet: 0.48 (0.28), residues: 339 loop : -0.40 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 208 TYR 0.024 0.002 TYR C 184 PHE 0.024 0.002 PHE C 235 TRP 0.031 0.002 TRP B 237 HIS 0.006 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 (23142) covalent geometry : angle 0.72462 / 0.37 (31314) hydrogen bonds : bond 0.05288 / 3.58 ( 1080) hydrogen bonds : angle 5.42990 / 3.87 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9472.87 seconds wall clock time: 161 minutes 47.67 seconds (9707.67 seconds total)