Starting phenix.real_space_refine on Tue Aug 26 14:14:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr4_40719/08_2025/8sr4_40719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr4_40719/08_2025/8sr4_40719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sr4_40719/08_2025/8sr4_40719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr4_40719/08_2025/8sr4_40719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sr4_40719/08_2025/8sr4_40719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr4_40719/08_2025/8sr4_40719.map" } resolution = 3.12 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= 0.003 sd= 0.024 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: 5 Type Number sf(0) Gaussians Cu 9 5.60 5 S 93 5.16 5 C 13818 2.51 5 N 3381 2.21 5 O 3606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20907 Number of models: 1 Model: "" Number of chains: 5 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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: E, I, F, J, G, K Time building chain proxies: 3.77, per 1000 atoms: 0.18 Number of scatterers: 20907 At special positions: 0 Unit cell: (107.407, 107.936, 117.989, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 9 28.99 S 93 16.00 O 3606 8.00 N 3381 7.00 C 13818 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: 1.34 Conformation dependent library (CDL) restraints added in 874.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 90 helices and 24 sheets defined 51.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 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: 3.962A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 45 removed outlier: 3.696A pdb=" N ALA B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.961A 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: 4.196A 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: 4.377A 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 211 through 239 removed outlier: 3.883A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 73 removed outlier: 3.602A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 114 removed outlier: 5.244A pdb=" N ASN C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE C 92 " --> pdb=" O TYR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 150 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 179 through 199 Processing helix chain 'C' and resid 208 through 224 Proline residue: C 217 - end of helix removed outlier: 4.203A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.727A pdb=" N TRP C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.529A pdb=" N ALA C 255 " --> pdb=" O GLY C 252 " (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: 3.962A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 4.135A 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: 3.961A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 45 removed outlier: 3.695A pdb=" N ALA F 14 " --> pdb=" O SER F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.961A 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: 4.197A 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: 4.377A 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 211 through 239 removed outlier: 3.883A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 45 removed outlier: 3.696A pdb=" N ALA J 14 " --> pdb=" O SER J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.961A 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: 4.196A 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: 4.377A 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 211 through 239 removed outlier: 3.884A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 73 removed outlier: 3.601A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 114 removed outlier: 5.244A pdb=" N ASN G 91 " --> pdb=" O THR G 87 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE G 92 " --> pdb=" O TYR G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 150 Processing helix chain 'G' and resid 150 through 161 Processing helix chain 'G' and resid 170 through 176 Processing helix chain 'G' and resid 179 through 199 Processing helix chain 'G' and resid 208 through 224 Proline residue: G 217 - end of helix removed outlier: 4.203A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix Processing helix chain 'G' and resid 225 through 233 removed outlier: 3.726A pdb=" N TRP G 229 " --> pdb=" O GLY G 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY G 230 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 removed outlier: 3.529A pdb=" N ALA G 255 " --> pdb=" O GLY G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 49 through 73 removed outlier: 3.602A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 removed outlier: 5.244A pdb=" N ASN K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE K 92 " --> pdb=" O TYR K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 150 Processing helix chain 'K' and resid 150 through 161 Processing helix chain 'K' and resid 170 through 176 Processing helix chain 'K' and resid 179 through 199 Processing helix chain 'K' and resid 208 through 224 Proline residue: K 217 - end of helix removed outlier: 4.203A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix Processing helix chain 'K' and resid 225 through 233 removed outlier: 3.727A pdb=" N TRP K 229 " --> pdb=" O GLY K 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 256 removed outlier: 3.529A pdb=" N ALA K 255 " --> pdb=" O GLY K 252 " (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: 4.253A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.607A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 348 removed outlier: 5.669A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342 removed outlier: 5.070A pdb=" N LEU A 314 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE A 394 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA8, first strand: chain 'B' and resid 243 through 244 Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.253A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AB2, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AB3, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB4, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.669A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 341 through 342 removed outlier: 5.070A pdb=" N LEU E 314 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE E 394 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.254A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 58 through 60 Processing sheet with id=AB8, first strand: chain 'I' and resid 87 through 90 Processing sheet with id=AB9, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AC1, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.669A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 341 through 342 removed outlier: 5.070A pdb=" N LEU I 314 " --> pdb=" O PHE I 394 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE I 394 " --> pdb=" O LEU I 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AC4, first strand: chain 'F' and resid 243 through 244 Processing sheet with id=AC5, first strand: chain 'J' and resid 170 through 173 Processing sheet with id=AC6, first strand: chain 'J' and resid 243 through 244 1098 hydrogen bonds defined for protein. 3204 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: 3.27 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3170 1.31 - 1.43: 6679 1.43 - 1.56: 11580 1.56 - 1.68: 0 1.68 - 1.81: 180 Bond restraints: 21609 Sorted by residual: bond pdb=" CE1 HIS A 48 " pdb=" NE2 HIS A 48 " ideal model delta sigma weight residual 1.321 1.378 -0.057 1.00e-02 1.00e+04 3.21e+01 bond pdb=" CE1 HIS E 48 " pdb=" NE2 HIS E 48 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.19e+01 bond pdb=" CE1 HIS I 48 " pdb=" NE2 HIS I 48 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.16e+01 bond pdb=" CG HIS E 48 " pdb=" ND1 HIS E 48 " ideal model delta sigma weight residual 1.378 1.431 -0.053 1.10e-02 8.26e+03 2.33e+01 bond pdb=" CG HIS I 48 " pdb=" ND1 HIS I 48 " ideal model delta sigma weight residual 1.378 1.431 -0.053 1.10e-02 8.26e+03 2.31e+01 ... (remaining 21604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 27658 1.51 - 3.01: 1517 3.01 - 4.52: 249 4.52 - 6.03: 72 6.03 - 7.53: 9 Bond angle restraints: 29505 Sorted by residual: angle pdb=" N PHE C 248 " pdb=" CA PHE C 248 " pdb=" C PHE C 248 " ideal model delta sigma weight residual 113.97 107.23 6.74 1.28e+00 6.10e-01 2.77e+01 angle pdb=" N PHE G 248 " pdb=" CA PHE G 248 " pdb=" C PHE G 248 " ideal model delta sigma weight residual 113.97 107.24 6.73 1.28e+00 6.10e-01 2.76e+01 angle pdb=" N PHE K 248 " pdb=" CA PHE K 248 " pdb=" C PHE K 248 " ideal model delta sigma weight residual 113.97 107.26 6.71 1.28e+00 6.10e-01 2.75e+01 angle pdb=" C LEU B 124 " pdb=" N VAL B 125 " pdb=" CA VAL B 125 " ideal model delta sigma weight residual 120.24 123.41 -3.17 6.30e-01 2.52e+00 2.53e+01 angle pdb=" C LEU J 124 " pdb=" N VAL J 125 " pdb=" CA VAL J 125 " ideal model delta sigma weight residual 120.24 123.40 -3.16 6.30e-01 2.52e+00 2.52e+01 ... (remaining 29500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 11005 17.46 - 34.93: 1004 34.93 - 52.39: 144 52.39 - 69.85: 48 69.85 - 87.32: 18 Dihedral angle restraints: 12219 sinusoidal: 4767 harmonic: 7452 Sorted by residual: dihedral pdb=" CA ILE E 211 " pdb=" C ILE E 211 " pdb=" N PHE E 212 " pdb=" CA PHE E 212 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ILE A 211 " pdb=" C ILE A 211 " pdb=" N PHE A 212 " pdb=" CA PHE A 212 " ideal model delta harmonic sigma weight residual 180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ILE I 211 " pdb=" C ILE I 211 " pdb=" N PHE I 212 " pdb=" CA PHE I 212 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 12216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2424 0.056 - 0.112: 624 0.112 - 0.168: 84 0.168 - 0.224: 33 0.224 - 0.280: 6 Chirality restraints: 3171 Sorted by residual: chirality pdb=" CA HIS C 231 " pdb=" N HIS C 231 " pdb=" C HIS C 231 " pdb=" CB HIS C 231 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA HIS G 231 " pdb=" N HIS G 231 " pdb=" C HIS G 231 " pdb=" CB HIS G 231 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA HIS K 231 " pdb=" N HIS K 231 " pdb=" C HIS K 231 " pdb=" CB HIS K 231 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 3168 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 72 " -0.030 2.00e-02 2.50e+03 2.75e-02 1.13e+01 pdb=" CG HIS I 72 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS I 72 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS I 72 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS I 72 " -0.040 2.00e-02 2.50e+03 pdb=" NE2 HIS I 72 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 72 " -0.030 2.00e-02 2.50e+03 2.73e-02 1.12e+01 pdb=" CG HIS A 72 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS A 72 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS A 72 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 72 " -0.040 2.00e-02 2.50e+03 pdb=" NE2 HIS A 72 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 72 " -0.030 2.00e-02 2.50e+03 2.72e-02 1.11e+01 pdb=" CG HIS E 72 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS E 72 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS E 72 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS E 72 " -0.040 2.00e-02 2.50e+03 pdb=" NE2 HIS E 72 " 0.000 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 30 2.11 - 2.81: 5939 2.81 - 3.51: 31466 3.51 - 4.20: 54059 4.20 - 4.90: 94743 Nonbonded interactions: 186237 Sorted by model distance: nonbonded pdb=" O GLU C 237 " pdb=" NH1 ARG F 206 " model vdw 1.413 3.120 nonbonded pdb=" NH1 ARG J 206 " pdb=" O GLU G 237 " model vdw 1.530 3.120 nonbonded pdb=" NH1 ARG B 206 " pdb=" O GLU K 237 " model vdw 1.648 3.120 nonbonded pdb=" NE2 GLN E 404 " pdb="CU CU E 502 " model vdw 1.650 2.320 nonbonded pdb=" NE2 GLN A 404 " pdb="CU CU A 502 " model vdw 1.651 2.320 ... (remaining 186232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } 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: 11.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.630 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.005 0.069 21609 Z= 0.337 Angle : 0.782 7.533 29505 Z= 0.489 Chirality : 0.053 0.280 3171 Planarity : 0.005 0.041 3660 Dihedral : 13.995 87.316 7461 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.23 % Favored : 92.07 % Rotamer: Outliers : 2.19 % Allowed : 2.42 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2559 helix: 0.86 (0.16), residues: 1152 sheet: 0.04 (0.28), residues: 378 loop : -0.81 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 375 TYR 0.015 0.002 TYR J 37 PHE 0.015 0.001 PHE G 169 TRP 0.029 0.002 TRP K 229 HIS 0.025 0.003 HIS I 72 Details of bonding type rmsd covalent geometry : bond 0.00526 (21609) covalent geometry : angle 0.78239 (29505) hydrogen bonds : bond 0.13323 ( 1098) hydrogen bonds : angle 6.77360 ( 3204) *********************** 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 395 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6765 (mp0) REVERT: A 141 MET cc_start: 0.8139 (ptp) cc_final: 0.7642 (ptp) REVERT: A 375 ARG cc_start: 0.7850 (mtt-85) cc_final: 0.7617 (mtp85) REVERT: B 11 HIS cc_start: 0.8367 (m-70) cc_final: 0.8102 (m90) REVERT: B 23 TRP cc_start: 0.6877 (m-10) cc_final: 0.6519 (m100) REVERT: B 44 THR cc_start: 0.7336 (p) cc_final: 0.7102 (p) REVERT: B 199 MET cc_start: 0.6734 (mtp) cc_final: 0.5758 (mtt) REVERT: C 113 LYS cc_start: 0.8269 (mptt) cc_final: 0.8057 (mptt) REVERT: C 126 GLU cc_start: 0.7703 (tm-30) cc_final: 0.6985 (tm-30) REVERT: E 117 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6795 (mp0) REVERT: E 375 ARG cc_start: 0.7852 (mtt-85) cc_final: 0.7602 (mtp85) REVERT: I 117 GLU cc_start: 0.7547 (mm-30) cc_final: 0.6742 (mp0) REVERT: I 375 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7583 (mtp85) REVERT: F 11 HIS cc_start: 0.8371 (m-70) cc_final: 0.8091 (m90) REVERT: F 23 TRP cc_start: 0.6829 (m-10) cc_final: 0.6474 (m100) REVERT: F 199 MET cc_start: 0.6772 (mtp) cc_final: 0.5913 (mtm) REVERT: J 11 HIS cc_start: 0.8374 (m-70) cc_final: 0.8126 (m90) REVERT: J 23 TRP cc_start: 0.6847 (m-10) cc_final: 0.6497 (m100) REVERT: J 44 THR cc_start: 0.7396 (p) cc_final: 0.7172 (p) REVERT: J 199 MET cc_start: 0.6796 (mtp) cc_final: 0.5810 (mtt) REVERT: G 113 LYS cc_start: 0.8218 (mptt) cc_final: 0.7987 (mptt) REVERT: G 126 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7282 (tp30) REVERT: K 113 LYS cc_start: 0.8239 (mptt) cc_final: 0.7980 (mptt) REVERT: K 126 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7109 (tp30) outliers start: 48 outliers final: 24 residues processed: 380 average time/residue: 0.1391 time to fit residues: 79.4266 Evaluate side-chains 256 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 177 PHE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 177 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 245 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: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN B 160 ASN E 108 GLN F 160 ASN F 245 GLN J 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091676 restraints weight = 29646.363| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.65 r_work: 0.2983 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21609 Z= 0.170 Angle : 0.615 7.174 29505 Z= 0.324 Chirality : 0.045 0.168 3171 Planarity : 0.005 0.046 3660 Dihedral : 6.814 71.429 2874 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.08 % Favored : 94.69 % Rotamer: Outliers : 2.19 % Allowed : 9.37 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.17), residues: 2559 helix: 0.82 (0.15), residues: 1182 sheet: 0.35 (0.29), residues: 360 loop : -0.47 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 198 TYR 0.031 0.002 TYR K 184 PHE 0.020 0.002 PHE K 251 TRP 0.025 0.002 TRP K 137 HIS 0.005 0.001 HIS I 72 Details of bonding type rmsd covalent geometry : bond 0.00393 (21609) covalent geometry : angle 0.61548 (29505) hydrogen bonds : bond 0.04282 ( 1098) hydrogen bonds : angle 5.44358 ( 3204) *********************** 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 294 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7733 (mp0) REVERT: A 141 MET cc_start: 0.8585 (ptp) cc_final: 0.8299 (ptp) REVERT: A 299 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7384 (ttp80) REVERT: A 375 ARG cc_start: 0.8323 (mtt-85) cc_final: 0.7937 (mtp85) REVERT: B 11 HIS cc_start: 0.8487 (m-70) cc_final: 0.8169 (m-70) REVERT: B 23 TRP cc_start: 0.7301 (m-10) cc_final: 0.6955 (m100) REVERT: B 199 MET cc_start: 0.7353 (mtp) cc_final: 0.6402 (mtt) REVERT: E 38 GLN cc_start: 0.8318 (mt0) cc_final: 0.8013 (mt0) REVERT: E 117 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7716 (mp0) REVERT: E 375 ARG cc_start: 0.8360 (mtt-85) cc_final: 0.8001 (mtp85) REVERT: E 406 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7787 (t70) REVERT: I 117 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7723 (mp0) REVERT: I 141 MET cc_start: 0.8759 (ptp) cc_final: 0.8484 (ptp) REVERT: I 375 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.7923 (mtp85) REVERT: F 11 HIS cc_start: 0.8441 (m-70) cc_final: 0.7948 (m-70) REVERT: F 23 TRP cc_start: 0.7272 (m-10) cc_final: 0.6853 (m100) REVERT: F 182 ASP cc_start: 0.8689 (m-30) cc_final: 0.8481 (m-30) REVERT: F 199 MET cc_start: 0.7315 (mtp) cc_final: 0.6491 (mtm) REVERT: F 230 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8420 (ptt) REVERT: J 11 HIS cc_start: 0.8459 (m-70) cc_final: 0.8020 (m-70) REVERT: J 23 TRP cc_start: 0.7336 (m-10) cc_final: 0.6963 (m100) REVERT: J 199 MET cc_start: 0.7344 (mtp) cc_final: 0.6342 (mtt) REVERT: J 230 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8380 (ptt) REVERT: K 113 LYS cc_start: 0.8252 (mptt) cc_final: 0.8023 (mptt) REVERT: K 154 GLU cc_start: 0.6363 (mm-30) cc_final: 0.6138 (mm-30) outliers start: 48 outliers final: 28 residues processed: 274 average time/residue: 0.1348 time to fit residues: 56.9089 Evaluate side-chains 250 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 209 optimal weight: 1.9990 chunk 123 optimal weight: 0.0030 chunk 96 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 224 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 160 ASN E 108 GLN E 401 GLN F 160 ASN J 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091074 restraints weight = 29943.193| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.66 r_work: 0.2961 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21609 Z= 0.155 Angle : 0.568 8.504 29505 Z= 0.298 Chirality : 0.044 0.140 3171 Planarity : 0.005 0.043 3660 Dihedral : 6.340 77.717 2860 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.16 % Favored : 94.61 % Rotamer: Outliers : 2.79 % Allowed : 11.07 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.17), residues: 2559 helix: 0.96 (0.15), residues: 1206 sheet: 0.47 (0.28), residues: 396 loop : -0.28 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 117 TYR 0.026 0.001 TYR K 184 PHE 0.019 0.001 PHE K 251 TRP 0.018 0.001 TRP G 137 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00360 (21609) covalent geometry : angle 0.56761 (29505) hydrogen bonds : bond 0.04036 ( 1098) hydrogen bonds : angle 5.22162 ( 3204) *********************** 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 292 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 231 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7727 (mp0) REVERT: A 163 MET cc_start: 0.8523 (ttt) cc_final: 0.8075 (ttt) REVERT: A 299 ARG cc_start: 0.7652 (ttm110) cc_final: 0.7442 (ttp80) REVERT: A 375 ARG cc_start: 0.8393 (mtt-85) cc_final: 0.7977 (mtp85) REVERT: A 382 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8904 (t70) REVERT: B 11 HIS cc_start: 0.8489 (m-70) cc_final: 0.8153 (m-70) REVERT: B 23 TRP cc_start: 0.7357 (m-10) cc_final: 0.7061 (m100) REVERT: B 199 MET cc_start: 0.7334 (mtp) cc_final: 0.6293 (mtt) REVERT: B 230 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8406 (ptt) REVERT: C 219 MET cc_start: 0.7138 (tpp) cc_final: 0.6687 (ttm) REVERT: E 117 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7743 (mp0) REVERT: E 375 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.7965 (mtp85) REVERT: E 406 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7779 (t70) REVERT: I 117 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7742 (mp0) REVERT: I 163 MET cc_start: 0.8568 (ttt) cc_final: 0.8078 (ttt) REVERT: I 375 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7921 (mtp85) REVERT: F 11 HIS cc_start: 0.8437 (m-70) cc_final: 0.8015 (m-70) REVERT: F 23 TRP cc_start: 0.7351 (m-10) cc_final: 0.6958 (m100) REVERT: F 182 ASP cc_start: 0.8639 (m-30) cc_final: 0.8417 (m-30) REVERT: F 199 MET cc_start: 0.7307 (mtp) cc_final: 0.6364 (mtt) REVERT: F 230 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8420 (ptt) REVERT: J 11 HIS cc_start: 0.8470 (m-70) cc_final: 0.8104 (m-70) REVERT: J 23 TRP cc_start: 0.7409 (m-10) cc_final: 0.7081 (m100) REVERT: J 199 MET cc_start: 0.7262 (mtp) cc_final: 0.6310 (mtt) REVERT: J 230 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8404 (ptt) REVERT: G 219 MET cc_start: 0.7523 (tpp) cc_final: 0.7228 (tpp) REVERT: G 241 VAL cc_start: 0.6516 (m) cc_final: 0.6245 (t) REVERT: K 241 VAL cc_start: 0.6573 (m) cc_final: 0.6305 (t) outliers start: 61 outliers final: 33 residues processed: 265 average time/residue: 0.1321 time to fit residues: 54.5110 Evaluate side-chains 257 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 187 ASN E 108 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN J 187 ASN J 245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.088172 restraints weight = 30692.105| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.72 r_work: 0.2872 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 21609 Z= 0.246 Angle : 0.613 5.910 29505 Z= 0.324 Chirality : 0.046 0.182 3171 Planarity : 0.005 0.042 3660 Dihedral : 5.760 59.961 2846 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.37 % Rotamer: Outliers : 2.47 % Allowed : 13.03 % Favored : 84.50 % 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 aren not related in a simple way. whole: 0.44 (0.17), residues: 2559 helix: 0.91 (0.15), residues: 1200 sheet: 0.28 (0.29), residues: 372 loop : -0.35 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 129 TYR 0.024 0.002 TYR G 184 PHE 0.025 0.002 PHE G 251 TRP 0.019 0.002 TRP G 137 HIS 0.004 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00589 (21609) covalent geometry : angle 0.61274 (29505) hydrogen bonds : bond 0.04411 ( 1098) hydrogen bonds : angle 5.21216 ( 3204) *********************** 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 283 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.512 Fit side-chains REVERT: A 117 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7790 (mp0) REVERT: A 141 MET cc_start: 0.8879 (ptp) cc_final: 0.8578 (ptm) REVERT: A 258 TYR cc_start: 0.7796 (m-10) cc_final: 0.7519 (m-10) REVERT: A 299 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7373 (ttp80) REVERT: A 375 ARG cc_start: 0.8448 (mtt-85) cc_final: 0.7987 (mtp85) REVERT: B 9 ARG cc_start: 0.8464 (mmt-90) cc_final: 0.8068 (mpt180) REVERT: B 11 HIS cc_start: 0.8554 (m-70) cc_final: 0.8165 (m-70) REVERT: B 23 TRP cc_start: 0.7404 (m-10) cc_final: 0.7077 (m100) REVERT: B 42 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7494 (mmm) REVERT: B 199 MET cc_start: 0.7424 (mtp) cc_final: 0.6825 (mtp) REVERT: B 205 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6227 (mm) REVERT: C 219 MET cc_start: 0.7281 (tpp) cc_final: 0.6961 (ttm) REVERT: E 117 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7823 (mp0) REVERT: E 163 MET cc_start: 0.8644 (ttt) cc_final: 0.8271 (ttt) REVERT: E 406 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7982 (t70) REVERT: I 117 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7830 (mp0) REVERT: I 141 MET cc_start: 0.8935 (ptp) cc_final: 0.8702 (ptm) REVERT: I 375 ARG cc_start: 0.8414 (mtt-85) cc_final: 0.7950 (mtp85) REVERT: F 9 ARG cc_start: 0.8471 (mmt-90) cc_final: 0.8074 (mpt180) REVERT: F 11 HIS cc_start: 0.8522 (m-70) cc_final: 0.8050 (m-70) REVERT: F 23 TRP cc_start: 0.7443 (m-10) cc_final: 0.7081 (m100) REVERT: F 182 ASP cc_start: 0.8675 (m-30) cc_final: 0.8464 (m-30) REVERT: F 199 MET cc_start: 0.7430 (mtp) cc_final: 0.6506 (mtt) REVERT: F 230 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8445 (ptt) REVERT: J 9 ARG cc_start: 0.8443 (mmt-90) cc_final: 0.8057 (mpt180) REVERT: J 11 HIS cc_start: 0.8519 (m-70) cc_final: 0.8135 (m-70) REVERT: J 23 TRP cc_start: 0.7441 (m-10) cc_final: 0.7119 (m100) REVERT: J 42 MET cc_start: 0.8044 (ttp) cc_final: 0.7615 (ttp) REVERT: J 178 MET cc_start: 0.9149 (mtp) cc_final: 0.8797 (mtp) REVERT: J 199 MET cc_start: 0.7379 (mtp) cc_final: 0.6469 (mtt) REVERT: J 230 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8419 (ptt) REVERT: G 219 MET cc_start: 0.7522 (tpp) cc_final: 0.7291 (tpp) REVERT: K 90 MET cc_start: 0.5460 (mmt) cc_final: 0.5002 (mmt) REVERT: K 113 LYS cc_start: 0.8169 (mptt) cc_final: 0.7936 (mptt) REVERT: K 219 MET cc_start: 0.7413 (tpp) cc_final: 0.7203 (tpp) REVERT: K 241 VAL cc_start: 0.6941 (m) cc_final: 0.6737 (t) outliers start: 54 outliers final: 35 residues processed: 262 average time/residue: 0.1361 time to fit residues: 54.7466 Evaluate side-chains 262 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 245 HIS Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 188 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 91 optimal weight: 0.0040 chunk 107 optimal weight: 0.6980 chunk 242 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS I 72 HIS I 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090265 restraints weight = 30030.789| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.68 r_work: 0.2946 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21609 Z= 0.131 Angle : 0.534 5.441 29505 Z= 0.282 Chirality : 0.043 0.156 3171 Planarity : 0.004 0.043 3660 Dihedral : 5.371 59.517 2841 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.04 % Rotamer: Outliers : 2.70 % Allowed : 13.67 % Favored : 83.63 % 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 aren not related in a simple way. whole: 0.57 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1206 sheet: 0.26 (0.27), residues: 408 loop : -0.28 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 129 TYR 0.025 0.001 TYR G 184 PHE 0.024 0.001 PHE G 251 TRP 0.016 0.001 TRP A 202 HIS 0.004 0.001 HIS J 232 Details of bonding type rmsd covalent geometry : bond 0.00294 (21609) covalent geometry : angle 0.53398 (29505) hydrogen bonds : bond 0.03855 ( 1098) hydrogen bonds : angle 5.05930 ( 3204) *********************** 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 293 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 234 time to evaluate : 0.764 Fit side-chains REVERT: A 117 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7755 (mp0) REVERT: A 299 ARG cc_start: 0.7605 (ttm110) cc_final: 0.7384 (ttp80) REVERT: A 375 ARG cc_start: 0.8444 (mtt-85) cc_final: 0.7967 (mtp85) REVERT: B 9 ARG cc_start: 0.8416 (mmt-90) cc_final: 0.8030 (mpt180) REVERT: B 11 HIS cc_start: 0.8498 (m-70) cc_final: 0.8160 (m-70) REVERT: B 23 TRP cc_start: 0.7390 (m-10) cc_final: 0.7118 (m100) REVERT: B 42 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7444 (mmm) REVERT: B 199 MET cc_start: 0.7364 (mtp) cc_final: 0.6325 (mtt) REVERT: B 205 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6122 (mm) REVERT: B 210 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7131 (tptt) REVERT: E 117 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7813 (mp0) REVERT: E 163 MET cc_start: 0.8558 (ttt) cc_final: 0.8133 (ttt) REVERT: E 239 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.6760 (m-80) REVERT: E 375 ARG cc_start: 0.8471 (mtt-85) cc_final: 0.7990 (mtp85) REVERT: E 406 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7806 (t70) REVERT: I 117 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7778 (mp0) REVERT: I 141 MET cc_start: 0.8900 (ptp) cc_final: 0.8552 (ptm) REVERT: I 163 MET cc_start: 0.8545 (ttt) cc_final: 0.8109 (ttt) REVERT: I 375 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.7966 (mtp85) REVERT: F 9 ARG cc_start: 0.8445 (mmt-90) cc_final: 0.8035 (mpt180) REVERT: F 11 HIS cc_start: 0.8478 (m-70) cc_final: 0.8012 (m-70) REVERT: F 23 TRP cc_start: 0.7410 (m-10) cc_final: 0.7073 (m100) REVERT: F 182 ASP cc_start: 0.8648 (m-30) cc_final: 0.8365 (m-30) REVERT: F 199 MET cc_start: 0.7320 (mtp) cc_final: 0.6408 (mtt) REVERT: F 230 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8410 (ptt) REVERT: J 9 ARG cc_start: 0.8446 (mmt-90) cc_final: 0.8020 (mpt180) REVERT: J 11 HIS cc_start: 0.8454 (m-70) cc_final: 0.8085 (m-70) REVERT: J 23 TRP cc_start: 0.7424 (m-10) cc_final: 0.7131 (m100) REVERT: J 42 MET cc_start: 0.7893 (ttp) cc_final: 0.7557 (ttp) REVERT: J 178 MET cc_start: 0.9097 (mtp) cc_final: 0.8823 (mtp) REVERT: J 199 MET cc_start: 0.7200 (mtp) cc_final: 0.6317 (mtt) REVERT: J 210 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7116 (tptt) REVERT: J 230 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8420 (ptt) REVERT: K 113 LYS cc_start: 0.8165 (mptt) cc_final: 0.7938 (mptt) REVERT: K 219 MET cc_start: 0.7370 (tpp) cc_final: 0.7151 (tpp) outliers start: 59 outliers final: 34 residues processed: 273 average time/residue: 0.1402 time to fit residues: 58.9964 Evaluate side-chains 265 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 59 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 146 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 108 GLN A 404 GLN B 245 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 GLN F 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.088342 restraints weight = 30167.740| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.70 r_work: 0.2915 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21609 Z= 0.173 Angle : 0.561 7.681 29505 Z= 0.295 Chirality : 0.044 0.166 3171 Planarity : 0.005 0.045 3660 Dihedral : 5.120 57.924 2837 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 2.47 % Allowed : 14.59 % Favored : 82.94 % 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 aren not related in a simple way. whole: 0.58 (0.17), residues: 2559 helix: 1.11 (0.15), residues: 1191 sheet: 0.36 (0.28), residues: 372 loop : -0.38 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 129 TYR 0.025 0.002 TYR C 210 PHE 0.025 0.001 PHE K 251 TRP 0.021 0.001 TRP E 206 HIS 0.004 0.001 HIS J 232 Details of bonding type rmsd covalent geometry : bond 0.00407 (21609) covalent geometry : angle 0.56100 (29505) hydrogen bonds : bond 0.04042 ( 1098) hydrogen bonds : angle 5.06663 ( 3204) *********************** 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 283 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7747 (mp0) REVERT: A 375 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.7926 (mtp85) REVERT: B 9 ARG cc_start: 0.8467 (mmt-90) cc_final: 0.8017 (mpt180) REVERT: B 11 HIS cc_start: 0.8501 (m-70) cc_final: 0.8167 (m-70) REVERT: B 23 TRP cc_start: 0.7403 (m-10) cc_final: 0.7151 (m100) REVERT: B 42 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7448 (mmm) REVERT: B 199 MET cc_start: 0.7366 (mtp) cc_final: 0.6316 (mtt) REVERT: B 210 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7205 (tptt) REVERT: C 219 MET cc_start: 0.7078 (tpp) cc_final: 0.6681 (ttm) REVERT: C 241 VAL cc_start: 0.7053 (m) cc_final: 0.6850 (t) REVERT: E 117 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7797 (mp0) REVERT: E 375 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.7949 (mtp85) REVERT: E 406 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7842 (t70) REVERT: I 117 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7765 (mp0) REVERT: I 141 MET cc_start: 0.8967 (ptp) cc_final: 0.8700 (ptm) REVERT: I 176 GLN cc_start: 0.8618 (mt0) cc_final: 0.8231 (mm-40) REVERT: I 375 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.7935 (mtp85) REVERT: F 9 ARG cc_start: 0.8473 (mmt-90) cc_final: 0.8031 (mpt180) REVERT: F 11 HIS cc_start: 0.8478 (m-70) cc_final: 0.8006 (m-70) REVERT: F 23 TRP cc_start: 0.7432 (m-10) cc_final: 0.7125 (m100) REVERT: F 178 MET cc_start: 0.9091 (mtp) cc_final: 0.8675 (mtm) REVERT: F 199 MET cc_start: 0.7285 (mtp) cc_final: 0.6385 (mtt) REVERT: F 210 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7209 (tptt) REVERT: F 230 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8411 (ptt) REVERT: J 9 ARG cc_start: 0.8452 (mmt-90) cc_final: 0.7997 (mpt180) REVERT: J 11 HIS cc_start: 0.8467 (m-70) cc_final: 0.8105 (m-70) REVERT: J 23 TRP cc_start: 0.7414 (m-10) cc_final: 0.7181 (m100) REVERT: J 42 MET cc_start: 0.8003 (ttp) cc_final: 0.7607 (ttm) REVERT: J 178 MET cc_start: 0.9089 (mtp) cc_final: 0.8848 (mtt) REVERT: J 199 MET cc_start: 0.7230 (mtp) cc_final: 0.6333 (mtt) REVERT: J 210 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7179 (tptt) REVERT: J 230 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8437 (ptt) REVERT: G 219 MET cc_start: 0.7427 (tpp) cc_final: 0.6825 (tpp) REVERT: K 90 MET cc_start: 0.5441 (mmt) cc_final: 0.4947 (mmt) outliers start: 54 outliers final: 38 residues processed: 264 average time/residue: 0.1376 time to fit residues: 56.1532 Evaluate side-chains 265 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 192 optimal weight: 0.9990 chunk 227 optimal weight: 20.0000 chunk 199 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.088039 restraints weight = 30590.310| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.69 r_work: 0.2892 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21609 Z= 0.193 Angle : 0.572 7.284 29505 Z= 0.300 Chirality : 0.045 0.139 3171 Planarity : 0.005 0.046 3660 Dihedral : 5.106 58.061 2837 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.92 % Rotamer: Outliers : 2.42 % Allowed : 15.13 % Favored : 82.44 % 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 aren not related in a simple way. whole: 0.57 (0.17), residues: 2559 helix: 1.11 (0.15), residues: 1191 sheet: 0.37 (0.28), residues: 372 loop : -0.41 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 299 TYR 0.026 0.002 TYR C 210 PHE 0.022 0.001 PHE K 251 TRP 0.020 0.001 TRP E 206 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00457 (21609) covalent geometry : angle 0.57152 (29505) hydrogen bonds : bond 0.04104 ( 1098) hydrogen bonds : angle 5.06891 ( 3204) *********************** 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 284 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7796 (mp0) REVERT: A 176 GLN cc_start: 0.8638 (mt0) cc_final: 0.8227 (mm-40) REVERT: A 375 ARG cc_start: 0.8476 (mtt-85) cc_final: 0.7993 (mtp85) REVERT: B 9 ARG cc_start: 0.8532 (mmt-90) cc_final: 0.7965 (mpt180) REVERT: B 11 HIS cc_start: 0.8533 (m-70) cc_final: 0.8175 (m-70) REVERT: B 23 TRP cc_start: 0.7440 (m-10) cc_final: 0.7209 (m100) REVERT: B 42 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7325 (mmm) REVERT: B 199 MET cc_start: 0.7464 (mtp) cc_final: 0.6886 (mtp) REVERT: B 210 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7173 (tptt) REVERT: C 219 MET cc_start: 0.7078 (tpp) cc_final: 0.6831 (ttm) REVERT: C 241 VAL cc_start: 0.7150 (m) cc_final: 0.6948 (t) REVERT: E 117 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7848 (mp0) REVERT: E 206 TRP cc_start: 0.8721 (m100) cc_final: 0.8381 (m100) REVERT: E 239 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: E 375 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.7981 (mtp85) REVERT: E 406 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7895 (t70) REVERT: I 117 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7828 (mp0) REVERT: I 141 MET cc_start: 0.9009 (ptp) cc_final: 0.8594 (ptm) REVERT: I 176 GLN cc_start: 0.8641 (mt0) cc_final: 0.8272 (mm-40) REVERT: I 375 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.7979 (mtp85) REVERT: F 9 ARG cc_start: 0.8525 (mmt-90) cc_final: 0.7968 (mpt180) REVERT: F 11 HIS cc_start: 0.8522 (m-70) cc_final: 0.8054 (m-70) REVERT: F 23 TRP cc_start: 0.7451 (m-10) cc_final: 0.7158 (m100) REVERT: F 178 MET cc_start: 0.9105 (mtp) cc_final: 0.8716 (mtm) REVERT: F 199 MET cc_start: 0.7344 (mtp) cc_final: 0.6450 (mtt) REVERT: F 210 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7308 (tptt) REVERT: F 230 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (ptt) REVERT: J 9 ARG cc_start: 0.8530 (mmt-90) cc_final: 0.7994 (mpt180) REVERT: J 11 HIS cc_start: 0.8478 (m-70) cc_final: 0.8080 (m-70) REVERT: J 23 TRP cc_start: 0.7442 (m-10) cc_final: 0.7227 (m100) REVERT: J 42 MET cc_start: 0.8016 (ttp) cc_final: 0.7692 (ttm) REVERT: J 199 MET cc_start: 0.7345 (mtp) cc_final: 0.6770 (mtp) REVERT: J 210 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7198 (tptt) REVERT: J 230 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8475 (ptt) REVERT: K 90 MET cc_start: 0.5444 (mmt) cc_final: 0.4968 (mmt) REVERT: K 113 LYS cc_start: 0.8130 (mptt) cc_final: 0.7915 (mptt) REVERT: K 219 MET cc_start: 0.7390 (tpp) cc_final: 0.6834 (tpp) outliers start: 53 outliers final: 38 residues processed: 269 average time/residue: 0.1251 time to fit residues: 52.1764 Evaluate side-chains 263 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 218 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 242 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 172 optimal weight: 0.0170 chunk 50 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 124 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 404 GLN C 161 GLN E 72 HIS E 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.092228 restraints weight = 30001.453| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.69 r_work: 0.2975 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21609 Z= 0.118 Angle : 0.532 6.731 29505 Z= 0.277 Chirality : 0.043 0.187 3171 Planarity : 0.005 0.046 3660 Dihedral : 4.770 48.280 2834 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 2.15 % Allowed : 15.64 % Favored : 82.21 % 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 aren not related in a simple way. whole: 0.70 (0.17), residues: 2559 helix: 1.23 (0.15), residues: 1200 sheet: 0.26 (0.26), residues: 423 loop : -0.32 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 299 TYR 0.023 0.001 TYR G 184 PHE 0.021 0.001 PHE G 251 TRP 0.018 0.001 TRP E 206 HIS 0.003 0.001 HIS J 232 Details of bonding type rmsd covalent geometry : bond 0.00262 (21609) covalent geometry : angle 0.53172 (29505) hydrogen bonds : bond 0.03629 ( 1098) hydrogen bonds : angle 4.89850 ( 3204) *********************** 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 285 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7791 (mp0) REVERT: A 176 GLN cc_start: 0.8638 (mt0) cc_final: 0.8246 (mm-40) REVERT: A 251 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8283 (ttt) REVERT: A 258 TYR cc_start: 0.7355 (m-10) cc_final: 0.7108 (m-10) REVERT: A 299 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7348 (ttp80) REVERT: A 375 ARG cc_start: 0.8502 (mtt-85) cc_final: 0.8068 (mtp85) REVERT: B 9 ARG cc_start: 0.8497 (mmt-90) cc_final: 0.7890 (mpt180) REVERT: B 11 HIS cc_start: 0.8500 (m-70) cc_final: 0.8141 (m-70) REVERT: B 23 TRP cc_start: 0.7388 (m-10) cc_final: 0.7183 (m100) REVERT: B 42 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7532 (mmm) REVERT: B 178 MET cc_start: 0.9090 (mtp) cc_final: 0.8858 (mtp) REVERT: B 199 MET cc_start: 0.7305 (mtp) cc_final: 0.6540 (mtp) REVERT: B 210 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7173 (tptt) REVERT: C 210 TYR cc_start: 0.8581 (t80) cc_final: 0.8133 (t80) REVERT: E 117 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7847 (mp0) REVERT: E 176 GLN cc_start: 0.8657 (mt0) cc_final: 0.8280 (mm-40) REVERT: E 206 TRP cc_start: 0.8629 (m100) cc_final: 0.8268 (m100) REVERT: E 239 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: E 251 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8285 (ttt) REVERT: E 375 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.7995 (mtp85) REVERT: E 406 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7709 (t70) REVERT: I 117 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7787 (mp0) REVERT: I 141 MET cc_start: 0.8926 (ptp) cc_final: 0.8529 (ptm) REVERT: I 163 MET cc_start: 0.8492 (ttt) cc_final: 0.8076 (ttt) REVERT: I 176 GLN cc_start: 0.8629 (mt0) cc_final: 0.8276 (mm-40) REVERT: I 206 TRP cc_start: 0.8577 (m100) cc_final: 0.8313 (m100) REVERT: I 258 TYR cc_start: 0.7397 (m-10) cc_final: 0.7185 (m-10) REVERT: I 375 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.7998 (mtp85) REVERT: F 9 ARG cc_start: 0.8496 (mmt-90) cc_final: 0.7933 (mpt180) REVERT: F 11 HIS cc_start: 0.8457 (m-70) cc_final: 0.8036 (m-70) REVERT: F 23 TRP cc_start: 0.7376 (m-10) cc_final: 0.7165 (m100) REVERT: F 199 MET cc_start: 0.7206 (mtp) cc_final: 0.6129 (mtt) REVERT: F 210 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7242 (tptt) REVERT: F 230 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8415 (ptt) REVERT: J 9 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.7961 (mpt180) REVERT: J 11 HIS cc_start: 0.8437 (m-70) cc_final: 0.8102 (m-70) REVERT: J 42 MET cc_start: 0.7903 (ttp) cc_final: 0.7662 (ttm) REVERT: J 199 MET cc_start: 0.7197 (mtp) cc_final: 0.6490 (mtp) REVERT: J 210 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7178 (tptt) REVERT: G 219 MET cc_start: 0.7307 (tpp) cc_final: 0.6721 (tpp) REVERT: K 113 LYS cc_start: 0.8103 (mptt) cc_final: 0.7897 (mptt) REVERT: K 219 MET cc_start: 0.7274 (tpp) cc_final: 0.6679 (tpp) outliers start: 47 outliers final: 32 residues processed: 267 average time/residue: 0.1381 time to fit residues: 57.0001 Evaluate side-chains 261 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 40 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN E 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087094 restraints weight = 30582.548| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.70 r_work: 0.2868 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 21609 Z= 0.242 Angle : 0.619 9.919 29505 Z= 0.324 Chirality : 0.047 0.167 3171 Planarity : 0.005 0.048 3660 Dihedral : 4.946 48.020 2832 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.92 % Rotamer: Outliers : 2.10 % Allowed : 15.73 % Favored : 82.17 % 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 aren not related in a simple way. whole: 0.60 (0.17), residues: 2559 helix: 1.14 (0.15), residues: 1194 sheet: 0.12 (0.26), residues: 423 loop : -0.30 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 299 TYR 0.026 0.002 TYR C 210 PHE 0.021 0.002 PHE K 251 TRP 0.037 0.002 TRP B 54 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00574 (21609) covalent geometry : angle 0.61887 (29505) hydrogen bonds : bond 0.04288 ( 1098) hydrogen bonds : angle 5.02604 ( 3204) *********************** 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 258 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7802 (mp0) REVERT: A 176 GLN cc_start: 0.8617 (mt0) cc_final: 0.8236 (mm-40) REVERT: A 375 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.8074 (mtp85) REVERT: B 9 ARG cc_start: 0.8545 (mmt-90) cc_final: 0.7917 (mpt180) REVERT: B 11 HIS cc_start: 0.8540 (m-70) cc_final: 0.8172 (m-70) REVERT: B 42 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7405 (mmm) REVERT: B 199 MET cc_start: 0.7494 (mtp) cc_final: 0.6930 (mtp) REVERT: B 210 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7183 (tptt) REVERT: C 219 MET cc_start: 0.7129 (tpp) cc_final: 0.6733 (ttm) REVERT: E 117 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7868 (mp0) REVERT: E 176 GLN cc_start: 0.8667 (mt0) cc_final: 0.8291 (mm-40) REVERT: E 239 PHE cc_start: 0.7327 (m-10) cc_final: 0.7114 (m-80) REVERT: E 375 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.7986 (mtp85) REVERT: E 404 GLN cc_start: 0.6931 (tt0) cc_final: 0.6700 (tt0) REVERT: I 117 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7854 (mp0) REVERT: I 176 GLN cc_start: 0.8655 (mt0) cc_final: 0.8303 (mm-40) REVERT: I 375 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.7990 (mtp85) REVERT: F 9 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.7927 (mpt180) REVERT: F 11 HIS cc_start: 0.8542 (m-70) cc_final: 0.8074 (m-70) REVERT: F 100 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8026 (mt-10) REVERT: F 199 MET cc_start: 0.7410 (mtp) cc_final: 0.6855 (mtp) REVERT: F 210 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7251 (tptt) REVERT: F 230 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8461 (ptt) REVERT: J 9 ARG cc_start: 0.8524 (mmt-90) cc_final: 0.7902 (mpt180) REVERT: J 11 HIS cc_start: 0.8506 (m-70) cc_final: 0.8136 (m-70) REVERT: J 42 MET cc_start: 0.8024 (ttp) cc_final: 0.7749 (ttm) REVERT: J 178 MET cc_start: 0.9203 (mtp) cc_final: 0.8939 (mtp) REVERT: J 199 MET cc_start: 0.7392 (mtp) cc_final: 0.6836 (mtp) REVERT: J 210 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7274 (tptt) REVERT: J 230 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8505 (ptt) REVERT: G 219 MET cc_start: 0.7366 (tpp) cc_final: 0.6797 (tpp) REVERT: K 113 LYS cc_start: 0.8097 (mptt) cc_final: 0.7890 (mptt) REVERT: K 219 MET cc_start: 0.7344 (tpp) cc_final: 0.6775 (tpp) outliers start: 46 outliers final: 34 residues processed: 241 average time/residue: 0.1415 time to fit residues: 52.7525 Evaluate side-chains 247 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 101 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 179 optimal weight: 0.0980 chunk 153 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.091509 restraints weight = 30285.803| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.70 r_work: 0.2950 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21609 Z= 0.125 Angle : 0.549 9.799 29505 Z= 0.285 Chirality : 0.044 0.151 3171 Planarity : 0.005 0.048 3660 Dihedral : 4.809 47.593 2832 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 1.69 % Allowed : 16.46 % Favored : 81.85 % 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 aren not related in a simple way. whole: 0.70 (0.17), residues: 2559 helix: 1.20 (0.15), residues: 1203 sheet: 0.30 (0.27), residues: 387 loop : -0.28 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 299 TYR 0.024 0.001 TYR G 184 PHE 0.020 0.001 PHE K 251 TRP 0.026 0.001 TRP B 54 HIS 0.003 0.001 HIS F 232 Details of bonding type rmsd covalent geometry : bond 0.00282 (21609) covalent geometry : angle 0.54934 (29505) hydrogen bonds : bond 0.03713 ( 1098) hydrogen bonds : angle 4.92098 ( 3204) ********************** 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 261 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7807 (mp0) REVERT: A 176 GLN cc_start: 0.8632 (mt0) cc_final: 0.8263 (mm-40) REVERT: A 251 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8286 (ttt) REVERT: A 258 TYR cc_start: 0.7450 (m-10) cc_final: 0.7190 (m-10) REVERT: A 375 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.8015 (mtp85) REVERT: A 406 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7719 (t70) REVERT: B 9 ARG cc_start: 0.8525 (mmt-90) cc_final: 0.7923 (mpt180) REVERT: B 11 HIS cc_start: 0.8513 (m-70) cc_final: 0.8143 (m-70) REVERT: B 42 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7576 (mmm) REVERT: B 178 MET cc_start: 0.9119 (mtp) cc_final: 0.8858 (mtp) REVERT: B 199 MET cc_start: 0.7292 (mtp) cc_final: 0.6731 (mtp) REVERT: B 210 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7177 (tptt) REVERT: C 210 TYR cc_start: 0.8607 (t80) cc_final: 0.8190 (t80) REVERT: C 219 MET cc_start: 0.7102 (tpp) cc_final: 0.6764 (ttm) REVERT: E 117 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7856 (mp0) REVERT: E 176 GLN cc_start: 0.8655 (mt0) cc_final: 0.8288 (mm-40) REVERT: E 206 TRP cc_start: 0.8619 (m100) cc_final: 0.8283 (m100) REVERT: E 251 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8309 (ttt) REVERT: E 375 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.8008 (mtp85) REVERT: E 404 GLN cc_start: 0.7199 (tt0) cc_final: 0.6955 (tt0) REVERT: I 117 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7810 (mp0) REVERT: I 176 GLN cc_start: 0.8638 (mt0) cc_final: 0.8298 (mm-40) REVERT: I 258 TYR cc_start: 0.7478 (m-10) cc_final: 0.7160 (m-10) REVERT: I 375 ARG cc_start: 0.8489 (mtt-85) cc_final: 0.8007 (mtp85) REVERT: F 9 ARG cc_start: 0.8523 (mmt-90) cc_final: 0.7891 (mpt180) REVERT: F 11 HIS cc_start: 0.8502 (m-70) cc_final: 0.8064 (m-70) REVERT: F 100 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8007 (mt-10) REVERT: F 199 MET cc_start: 0.7205 (mtp) cc_final: 0.6638 (mtp) REVERT: F 210 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7240 (tptt) REVERT: F 230 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8414 (ptt) REVERT: J 9 ARG cc_start: 0.8492 (mmt-90) cc_final: 0.7857 (mpt180) REVERT: J 11 HIS cc_start: 0.8470 (m-70) cc_final: 0.8150 (m-70) REVERT: J 178 MET cc_start: 0.9175 (mtp) cc_final: 0.8951 (mtp) REVERT: J 199 MET cc_start: 0.7227 (mtp) cc_final: 0.6655 (mtp) REVERT: J 210 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7252 (tptt) REVERT: J 230 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8442 (ptt) REVERT: G 219 MET cc_start: 0.7355 (tpp) cc_final: 0.6791 (tpp) REVERT: K 113 LYS cc_start: 0.8065 (mptt) cc_final: 0.7851 (mptt) REVERT: K 219 MET cc_start: 0.7348 (tpp) cc_final: 0.6751 (tpp) outliers start: 37 outliers final: 28 residues processed: 249 average time/residue: 0.1404 time to fit residues: 54.1421 Evaluate side-chains 251 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 218 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.089544 restraints weight = 30294.284| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.69 r_work: 0.2922 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21609 Z= 0.161 Angle : 0.567 12.597 29505 Z= 0.293 Chirality : 0.045 0.161 3171 Planarity : 0.005 0.049 3660 Dihedral : 4.779 47.723 2832 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % Rotamer: Outliers : 2.15 % Allowed : 16.28 % Favored : 81.57 % 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 aren not related in a simple way. whole: 0.65 (0.17), residues: 2559 helix: 1.15 (0.15), residues: 1218 sheet: 0.32 (0.27), residues: 387 loop : -0.34 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 299 TYR 0.024 0.001 TYR G 184 PHE 0.017 0.001 PHE G 248 TRP 0.028 0.001 TRP B 54 HIS 0.003 0.001 HIS F 232 Details of bonding type rmsd covalent geometry : bond 0.00379 (21609) covalent geometry : angle 0.56675 (29505) hydrogen bonds : bond 0.03897 ( 1098) hydrogen bonds : angle 4.92755 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4016.32 seconds wall clock time: 69 minutes 49.84 seconds (4189.84 seconds total)