Starting phenix.real_space_refine on Sun May 3 09:26:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qpo_53276/05_2026/9qpo_53276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qpo_53276/05_2026/9qpo_53276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qpo_53276/05_2026/9qpo_53276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qpo_53276/05_2026/9qpo_53276.map" model { file = "/net/cci-nas-00/data/ceres_data/9qpo_53276/05_2026/9qpo_53276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qpo_53276/05_2026/9qpo_53276.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 7467 2.51 5 N 2063 2.21 5 O 2227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11801 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2881 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 356} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2877 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2889 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 357} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2950 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 125 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 4, 35 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N BTHR G 320 " occ=0.50 ... (5 atoms not shown) pdb=" CG2BTHR G 320 " occ=0.50 residue: pdb=" N BVAL G 321 " occ=0.50 ... (5 atoms not shown) pdb=" CG2BVAL G 321 " occ=0.50 residue: pdb=" N BPHE G 322 " occ=0.50 ... (9 atoms not shown) pdb=" CZ BPHE G 322 " occ=0.50 residue: pdb=" N BHIS G 323 " occ=0.50 ... (8 atoms not shown) pdb=" NE2BHIS G 323 " occ=0.50 residue: pdb=" N ATHR F 320 " occ=0.50 ... (5 atoms not shown) pdb=" CG2ATHR F 320 " occ=0.50 residue: pdb=" N AVAL F 321 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL F 321 " occ=0.50 residue: pdb=" N APHE F 322 " occ=0.50 ... (9 atoms not shown) pdb=" CZ APHE F 322 " occ=0.50 residue: pdb=" N AHIS F 323 " occ=0.50 ... (9 atoms not shown) pdb=" OXTAHIS F 323 " occ=0.50 Time building chain proxies: 3.15, per 1000 atoms: 0.27 Number of scatterers: 11801 At special positions: 0 Unit cell: (79.18, 87.32, 136.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2227 8.00 N 2063 7.00 C 7467 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: 0.76 Conformation dependent library (CDL) restraints added in 685.9 milliseconds 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 17 sheets defined 38.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 29 through 49 removed outlier: 4.033A pdb=" N GLN A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 151 through 171 Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.563A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.948A pdb=" N GLN A 256 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 308 removed outlier: 3.521A pdb=" N SER A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 356 through 364 removed outlier: 3.661A pdb=" N ARG A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'B' and resid 29 through 49 removed outlier: 3.975A pdb=" N GLN B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 151 through 171 removed outlier: 3.580A pdb=" N ASN B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 289 through 308 removed outlier: 3.888A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 356 through 365 removed outlier: 3.884A pdb=" N VAL B 361 " --> pdb=" O PRO B 357 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'C' and resid 29 through 49 removed outlier: 4.096A pdb=" N GLN C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 95 through 98 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.813A pdb=" N ILE C 130 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 171 removed outlier: 3.599A pdb=" N ASN C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.865A pdb=" N LYS C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 253 through 257 removed outlier: 4.084A pdb=" N GLN C 256 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 289 through 308 removed outlier: 4.121A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 353 Processing helix chain 'C' and resid 356 through 365 Processing helix chain 'C' and resid 371 through 376 removed outlier: 3.506A pdb=" N ALA C 375 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'D' and resid 29 through 49 removed outlier: 3.953A pdb=" N GLN D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 151 through 170 removed outlier: 3.647A pdb=" N ASN D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.572A pdb=" N LYS D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.749A pdb=" N LEU D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 257 removed outlier: 3.737A pdb=" N GLN D 256 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 308 removed outlier: 3.976A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 353 Processing helix chain 'D' and resid 356 through 365 removed outlier: 4.110A pdb=" N VAL D 361 " --> pdb=" O PRO D 357 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG D 362 " --> pdb=" O GLY D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'E' and resid 312 through 318 removed outlier: 3.790A pdb=" N ARG E 318 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 25 removed outlier: 5.655A pdb=" N ASP A 179 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLN A 187 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL A 200 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N MET A 189 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 198 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP A 191 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU A 196 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N ILE A 241 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS A 201 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N HIS A 243 " --> pdb=" O HIS A 201 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 203 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 111 removed outlier: 3.932A pdb=" N GLY A 69 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.822A pdb=" N PHE A 99 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 143 removed outlier: 3.901A pdb=" N SER A 329 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 25 removed outlier: 4.714A pdb=" N GLN B 208 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP B 179 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER B 206 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS B 181 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 204 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLN B 183 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR B 202 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR B 185 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL B 200 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN B 187 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ILE B 241 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N HIS B 201 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N HIS B 243 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 203 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 113 removed outlier: 6.300A pdb=" N ILE B 65 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA B 109 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 67 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU B 111 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY B 69 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLN B 113 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 71 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.787A pdb=" N PHE B 99 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 136 through 143 removed outlier: 3.695A pdb=" N SER B 329 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 18 through 25 removed outlier: 5.886A pdb=" N ASP C 179 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLN C 187 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL C 200 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N MET C 189 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 198 " --> pdb=" O MET C 189 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP C 191 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 196 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N ILE C 241 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS C 201 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N HIS C 243 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 203 " --> pdb=" O HIS C 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 61 removed outlier: 6.237A pdb=" N ILE C 65 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA C 109 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU C 67 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLU C 111 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 69 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.661A pdb=" N PHE C 99 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 143 removed outlier: 3.562A pdb=" N GLY C 136 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 329 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 25 Processing sheet with id=AB5, first strand: chain 'D' and resid 17 through 25 removed outlier: 5.825A pdb=" N ASP D 179 " --> pdb=" O GLN D 208 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLN D 187 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL D 200 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 105 through 113 removed outlier: 4.279A pdb=" N GLY D 69 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.538A pdb=" N ASP D 94 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 99 " --> pdb=" O ASP D 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 136 through 143 removed outlier: 3.722A pdb=" N GLY D 136 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 329 " --> pdb=" O SER D 319 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1479 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: 1.75 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3927 1.34 - 1.46: 2351 1.46 - 1.58: 5685 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 12027 Sorted by residual: bond pdb=" CA LEU D 167 " pdb=" C LEU D 167 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.35e-02 5.49e+03 3.04e+00 bond pdb=" CG ARG A 192 " pdb=" CD ARG A 192 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CB LYS B 394 " pdb=" CG LYS B 394 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" N ATHR F 320 " pdb=" CA ATHR F 320 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.56e+00 bond pdb=" N BTHR G 320 " pdb=" CA BTHR G 320 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.90e-02 2.77e+03 1.50e+00 ... (remaining 12022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15962 1.80 - 3.61: 277 3.61 - 5.41: 26 5.41 - 7.21: 1 7.21 - 9.01: 3 Bond angle restraints: 16269 Sorted by residual: angle pdb=" CB LYS B 394 " pdb=" CG LYS B 394 " pdb=" CD LYS B 394 " ideal model delta sigma weight residual 111.30 120.31 -9.01 2.30e+00 1.89e-01 1.54e+01 angle pdb=" N VAL B 251 " pdb=" CA VAL B 251 " pdb=" C VAL B 251 " ideal model delta sigma weight residual 112.12 108.95 3.17 8.40e-01 1.42e+00 1.42e+01 angle pdb=" CA ATHR F 320 " pdb=" CB ATHR F 320 " pdb=" OG1ATHR F 320 " ideal model delta sigma weight residual 109.60 104.75 4.85 1.50e+00 4.44e-01 1.05e+01 angle pdb=" CG ARG A 192 " pdb=" CD ARG A 192 " pdb=" NE ARG A 192 " ideal model delta sigma weight residual 112.00 119.11 -7.11 2.20e+00 2.07e-01 1.04e+01 angle pdb=" CA BTHR G 320 " pdb=" CB BTHR G 320 " pdb=" OG1BTHR G 320 " ideal model delta sigma weight residual 109.60 104.78 4.82 1.50e+00 4.44e-01 1.03e+01 ... (remaining 16264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6480 17.97 - 35.93: 552 35.93 - 53.90: 121 53.90 - 71.86: 28 71.86 - 89.83: 24 Dihedral angle restraints: 7205 sinusoidal: 2876 harmonic: 4329 Sorted by residual: dihedral pdb=" CA SER D 384 " pdb=" C SER D 384 " pdb=" N PHE D 385 " pdb=" CA PHE D 385 " ideal model delta harmonic sigma weight residual 180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ARG D 177 " pdb=" C ARG D 177 " pdb=" N PRO D 178 " pdb=" CA PRO D 178 " ideal model delta harmonic sigma weight residual 180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ILE A 370 " pdb=" C ILE A 370 " pdb=" N TYR A 371 " pdb=" CA TYR A 371 " ideal model delta harmonic sigma weight residual 180.00 -163.22 -16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 7202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1093 0.031 - 0.061: 444 0.061 - 0.092: 156 0.092 - 0.122: 104 0.122 - 0.153: 17 Chirality restraints: 1814 Sorted by residual: chirality pdb=" CB THR D 62 " pdb=" CA THR D 62 " pdb=" OG1 THR D 62 " pdb=" CG2 THR D 62 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CB THR C 62 " pdb=" CA THR C 62 " pdb=" OG1 THR C 62 " pdb=" CG2 THR C 62 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA THR C 62 " pdb=" N THR C 62 " pdb=" C THR C 62 " pdb=" CB THR C 62 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1811 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 317 " -0.013 2.00e-02 2.50e+03 1.07e-02 2.87e+00 pdb=" CG TRP E 317 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP E 317 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP E 317 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 317 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 317 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 317 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 317 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 317 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 150 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C 151 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 385 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO C 386 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 386 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 386 " -0.018 5.00e-02 4.00e+02 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1090 2.74 - 3.28: 11393 3.28 - 3.82: 19862 3.82 - 4.36: 24410 4.36 - 4.90: 42290 Nonbonded interactions: 99045 Sorted by model distance: nonbonded pdb=" OH TYR B 79 " pdb=" OE1 GLN B 112 " model vdw 2.205 3.040 nonbonded pdb=" O HIS B 334 " pdb=" OG1 THR B 337 " model vdw 2.212 3.040 nonbonded pdb=" N GLU D 147 " pdb=" OE1 GLU D 147 " model vdw 2.225 3.120 nonbonded pdb=" OD1 ASP C 286 " pdb=" OG1 THR C 288 " model vdw 2.242 3.040 nonbonded pdb=" O TYR B 287 " pdb=" OG SER B 293 " model vdw 2.245 3.040 ... (remaining 99040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 111 or (resid 112 through 113 and (name N or na \ me CA or name C or name O or name CB )) or resid 114 or (resid 126 through 127 a \ nd (name N or name CA or name C or name O or name CB )) or resid 128 through 147 \ or (resid 148 and (name N or name CA or name C or name O or name CB )) or resid \ 149 through 395)) selection = (chain 'B' and (resid 16 through 111 or (resid 112 through 113 and (name N or na \ me CA or name C or name O or name CB )) or resid 114 or (resid 126 through 127 a \ nd (name N or name CA or name C or name O or name CB )) or resid 128 through 395 \ )) selection = (chain 'C' and (resid 16 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )) or resid 114 or (resid 126 through 127 and (name N o \ r name CA or name C or name O or name CB )) or resid 128 through 147 or (resid 1 \ 48 and (name N or name CA or name C or name O or name CB )) or resid 149 through \ 395)) selection = (chain 'D' and (resid 16 through 111 or (resid 112 through 113 and (name N or na \ me CA or name C or name O or name CB )) or resid 114 or (resid 126 through 127 a \ nd (name N or name CA or name C or name O or name CB )) or resid 128 through 147 \ or (resid 148 and (name N or name CA or name C or name O or name CB )) or resid \ 149 through 395)) } ncs_group { reference = (chain 'F' and (resid 320 through 322 or (resid 323 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2)))) selection = chain 'G' } 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=0.50 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.900 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.003 0.042 12027 Z= 0.140 Angle : 0.579 9.013 16269 Z= 0.336 Chirality : 0.043 0.153 1814 Planarity : 0.003 0.036 2100 Dihedral : 15.172 89.830 4441 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.64 % Allowed : 14.43 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1495 helix: 1.32 (0.25), residues: 443 sheet: 1.04 (0.31), residues: 311 loop : -0.12 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 192 TYR 0.010 0.001 TYR D 271 PHE 0.008 0.001 APHE F 322 TRP 0.029 0.001 TRP E 317 HIS 0.010 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00286 (12027) covalent geometry : angle 0.57921 (16269) hydrogen bonds : bond 0.18217 ( 529) hydrogen bonds : angle 6.35723 ( 1479) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.487 Fit side-chains REVERT: A 70 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8202 (tt0) REVERT: A 192 ARG cc_start: 0.8240 (mmp80) cc_final: 0.7996 (mmp80) REVERT: B 189 MET cc_start: 0.8838 (ttp) cc_final: 0.8076 (tpp) REVERT: C 23 GLU cc_start: 0.8313 (tt0) cc_final: 0.8010 (tp30) REVERT: C 225 LYS cc_start: 0.8533 (mppt) cc_final: 0.8246 (mppt) REVERT: C 249 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7490 (ttm110) REVERT: C 258 ASP cc_start: 0.8459 (t0) cc_final: 0.8100 (m-30) outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 0.6128 time to fit residues: 43.5372 Evaluate side-chains 58 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain C residue 249 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS B 112 GLN C 334 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.088955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.070995 restraints weight = 27620.259| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.27 r_work: 0.2915 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12027 Z= 0.236 Angle : 0.559 6.615 16269 Z= 0.304 Chirality : 0.046 0.150 1814 Planarity : 0.004 0.037 2100 Dihedral : 4.831 42.011 1661 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.55 % Allowed : 11.64 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1495 helix: 1.31 (0.24), residues: 453 sheet: 1.18 (0.30), residues: 299 loop : -0.20 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 192 TYR 0.013 0.001 TYR D 188 PHE 0.011 0.001 PHE D 385 TRP 0.011 0.001 TRP E 317 HIS 0.007 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00546 (12027) covalent geometry : angle 0.55865 (16269) hydrogen bonds : bond 0.04673 ( 529) hydrogen bonds : angle 4.70548 ( 1479) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.437 Fit side-chains REVERT: A 70 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7851 (tt0) REVERT: A 252 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8285 (tp) REVERT: B 189 MET cc_start: 0.8809 (ttp) cc_final: 0.8019 (tpp) REVERT: C 225 LYS cc_start: 0.8641 (mppt) cc_final: 0.8359 (mppt) REVERT: C 249 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7510 (ttm110) REVERT: C 370 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8372 (tt) REVERT: E 318 ARG cc_start: 0.7188 (mpt180) cc_final: 0.6776 (mmt-90) outliers start: 32 outliers final: 12 residues processed: 86 average time/residue: 0.5706 time to fit residues: 53.7784 Evaluate side-chains 69 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 329 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 119 optimal weight: 0.0370 chunk 42 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS C 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072498 restraints weight = 27131.979| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.26 r_work: 0.2945 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12027 Z= 0.140 Angle : 0.486 5.513 16269 Z= 0.265 Chirality : 0.044 0.145 1814 Planarity : 0.003 0.037 2100 Dihedral : 4.589 43.736 1657 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.83 % Allowed : 12.68 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1495 helix: 1.54 (0.24), residues: 455 sheet: 1.16 (0.30), residues: 303 loop : -0.15 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 192 TYR 0.012 0.001 TYR B 287 PHE 0.008 0.001 PHE D 385 TRP 0.009 0.001 TRP A 387 HIS 0.004 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00323 (12027) covalent geometry : angle 0.48615 (16269) hydrogen bonds : bond 0.03891 ( 529) hydrogen bonds : angle 4.32850 ( 1479) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.499 Fit side-chains REVERT: A 70 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7614 (tt0) REVERT: A 252 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8253 (tp) REVERT: B 189 MET cc_start: 0.8796 (ttp) cc_final: 0.8000 (tpp) REVERT: C 189 MET cc_start: 0.8243 (tpt) cc_final: 0.7890 (tpt) REVERT: C 225 LYS cc_start: 0.8656 (mppt) cc_final: 0.8384 (mppt) REVERT: C 249 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7795 (tpt170) REVERT: C 370 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8341 (tt) REVERT: D 134 ASP cc_start: 0.8894 (t0) cc_final: 0.8667 (t0) REVERT: D 223 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8604 (tppp) REVERT: E 318 ARG cc_start: 0.7241 (mpt180) cc_final: 0.6861 (mmt-90) outliers start: 23 outliers final: 13 residues processed: 80 average time/residue: 0.5670 time to fit residues: 49.7623 Evaluate side-chains 73 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 361 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS C 334 HIS E 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073743 restraints weight = 26787.047| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.25 r_work: 0.2972 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12027 Z= 0.105 Angle : 0.454 6.432 16269 Z= 0.247 Chirality : 0.043 0.139 1814 Planarity : 0.003 0.036 2100 Dihedral : 4.353 44.986 1656 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.99 % Allowed : 12.60 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.22), residues: 1495 helix: 1.77 (0.24), residues: 455 sheet: 1.20 (0.30), residues: 307 loop : -0.09 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.014 0.001 TYR B 287 PHE 0.007 0.001 PHE D 385 TRP 0.009 0.001 TRP A 387 HIS 0.005 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00237 (12027) covalent geometry : angle 0.45419 (16269) hydrogen bonds : bond 0.03314 ( 529) hydrogen bonds : angle 4.07903 ( 1479) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 252 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8209 (tp) REVERT: B 189 MET cc_start: 0.8756 (ttp) cc_final: 0.7943 (tpp) REVERT: C 189 MET cc_start: 0.8232 (tpt) cc_final: 0.7880 (tpt) REVERT: C 192 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7778 (tpm170) REVERT: C 220 ASP cc_start: 0.9133 (t70) cc_final: 0.8790 (t0) REVERT: C 225 LYS cc_start: 0.8651 (mppt) cc_final: 0.8220 (mptt) REVERT: C 249 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7833 (tpt170) REVERT: C 370 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8308 (tt) REVERT: D 134 ASP cc_start: 0.8907 (t0) cc_final: 0.8646 (t0) REVERT: D 223 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8585 (tppp) REVERT: E 318 ARG cc_start: 0.7260 (mpt180) cc_final: 0.6874 (mmt-90) outliers start: 25 outliers final: 12 residues processed: 88 average time/residue: 0.6519 time to fit residues: 62.1041 Evaluate side-chains 71 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 361 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.0170 chunk 35 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS C 334 HIS E 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073777 restraints weight = 26792.072| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.25 r_work: 0.2973 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12027 Z= 0.105 Angle : 0.453 6.707 16269 Z= 0.245 Chirality : 0.043 0.139 1814 Planarity : 0.003 0.036 2100 Dihedral : 4.262 45.585 1656 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.83 % Allowed : 13.40 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.22), residues: 1495 helix: 1.89 (0.24), residues: 454 sheet: 1.15 (0.30), residues: 306 loop : -0.06 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.014 0.001 TYR B 287 PHE 0.007 0.001 PHE D 385 TRP 0.009 0.001 TRP E 317 HIS 0.007 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00243 (12027) covalent geometry : angle 0.45280 (16269) hydrogen bonds : bond 0.03202 ( 529) hydrogen bonds : angle 4.01320 ( 1479) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8127 (mptp) REVERT: A 252 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8185 (tp) REVERT: B 189 MET cc_start: 0.8762 (ttp) cc_final: 0.7962 (tpp) REVERT: C 189 MET cc_start: 0.8236 (tpt) cc_final: 0.7862 (tpt) REVERT: C 220 ASP cc_start: 0.9097 (t70) cc_final: 0.8777 (t0) REVERT: C 225 LYS cc_start: 0.8609 (mppt) cc_final: 0.8153 (mptt) REVERT: C 249 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7800 (tpt170) REVERT: C 370 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8305 (tt) REVERT: D 134 ASP cc_start: 0.8950 (t0) cc_final: 0.8665 (t0) REVERT: D 223 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8546 (tppp) REVERT: E 318 ARG cc_start: 0.7292 (mpt180) cc_final: 0.6941 (mmt-90) outliers start: 23 outliers final: 11 residues processed: 78 average time/residue: 0.5354 time to fit residues: 46.1637 Evaluate side-chains 67 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 361 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS E 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073671 restraints weight = 27343.553| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.26 r_work: 0.2973 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12027 Z= 0.113 Angle : 0.451 6.283 16269 Z= 0.243 Chirality : 0.043 0.138 1814 Planarity : 0.003 0.035 2100 Dihedral : 4.196 46.237 1656 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.07 % Allowed : 13.80 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.22), residues: 1495 helix: 1.94 (0.24), residues: 455 sheet: 1.16 (0.30), residues: 308 loop : -0.05 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 192 TYR 0.013 0.001 TYR B 287 PHE 0.008 0.001 PHE D 385 TRP 0.008 0.001 TRP E 317 HIS 0.007 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00263 (12027) covalent geometry : angle 0.45085 (16269) hydrogen bonds : bond 0.03203 ( 529) hydrogen bonds : angle 3.96676 ( 1479) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.547 Fit side-chains REVERT: A 32 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8137 (mptp) REVERT: A 70 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 252 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8131 (tp) REVERT: B 189 MET cc_start: 0.8740 (ttp) cc_final: 0.7931 (tpp) REVERT: C 189 MET cc_start: 0.8276 (tpt) cc_final: 0.7991 (tpt) REVERT: C 192 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7834 (tpm170) REVERT: C 220 ASP cc_start: 0.9078 (t70) cc_final: 0.8779 (t0) REVERT: C 225 LYS cc_start: 0.8677 (mppt) cc_final: 0.8252 (mptt) REVERT: C 249 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7763 (tpt170) REVERT: C 370 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8327 (tt) REVERT: D 134 ASP cc_start: 0.8963 (t0) cc_final: 0.8700 (t0) REVERT: E 318 ARG cc_start: 0.7331 (mpt180) cc_final: 0.6977 (mmt-90) outliers start: 26 outliers final: 13 residues processed: 79 average time/residue: 0.6585 time to fit residues: 56.4496 Evaluate side-chains 70 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 361 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 99 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS E 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.072906 restraints weight = 27605.027| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.26 r_work: 0.2957 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12027 Z= 0.144 Angle : 0.473 8.030 16269 Z= 0.254 Chirality : 0.044 0.147 1814 Planarity : 0.003 0.036 2100 Dihedral : 4.251 47.233 1656 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.07 % Allowed : 14.19 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.22), residues: 1495 helix: 1.91 (0.24), residues: 456 sheet: 1.12 (0.30), residues: 306 loop : -0.06 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 192 TYR 0.015 0.001 TYR C 287 PHE 0.010 0.001 PHE D 385 TRP 0.013 0.001 TRP E 317 HIS 0.007 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00338 (12027) covalent geometry : angle 0.47287 (16269) hydrogen bonds : bond 0.03413 ( 529) hydrogen bonds : angle 3.99954 ( 1479) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.492 Fit side-chains REVERT: A 32 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8163 (mptp) REVERT: A 70 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7866 (mt-10) REVERT: A 252 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8157 (tp) REVERT: B 189 MET cc_start: 0.8754 (ttp) cc_final: 0.7946 (tpp) REVERT: C 189 MET cc_start: 0.8237 (tpt) cc_final: 0.7937 (tpt) REVERT: C 192 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7796 (tpm170) REVERT: C 220 ASP cc_start: 0.9077 (t70) cc_final: 0.8766 (t0) REVERT: C 225 LYS cc_start: 0.8671 (mppt) cc_final: 0.8225 (mptt) REVERT: C 249 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7786 (tpt170) REVERT: C 370 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8366 (tt) REVERT: D 134 ASP cc_start: 0.8959 (t0) cc_final: 0.8715 (t0) REVERT: E 318 ARG cc_start: 0.7392 (mpt180) cc_final: 0.6914 (mmt-90) outliers start: 26 outliers final: 14 residues processed: 76 average time/residue: 0.5979 time to fit residues: 49.6523 Evaluate side-chains 72 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 361 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 4 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS E 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073535 restraints weight = 26846.498| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.23 r_work: 0.2973 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12027 Z= 0.114 Angle : 0.458 7.215 16269 Z= 0.245 Chirality : 0.043 0.146 1814 Planarity : 0.003 0.036 2100 Dihedral : 4.187 48.401 1656 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.75 % Allowed : 14.43 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.22), residues: 1495 helix: 1.96 (0.24), residues: 456 sheet: 1.16 (0.30), residues: 306 loop : -0.06 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 192 TYR 0.013 0.001 TYR B 287 PHE 0.008 0.001 PHE D 385 TRP 0.014 0.001 TRP E 317 HIS 0.007 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00265 (12027) covalent geometry : angle 0.45767 (16269) hydrogen bonds : bond 0.03214 ( 529) hydrogen bonds : angle 3.95219 ( 1479) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.512 Fit side-chains REVERT: A 32 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8131 (mptp) REVERT: A 70 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 252 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8127 (tp) REVERT: B 189 MET cc_start: 0.8749 (ttp) cc_final: 0.7944 (tpp) REVERT: C 33 ILE cc_start: 0.8709 (mt) cc_final: 0.8459 (mt) REVERT: C 189 MET cc_start: 0.8194 (tpt) cc_final: 0.7886 (tpt) REVERT: C 192 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7801 (tpm170) REVERT: C 220 ASP cc_start: 0.9061 (t70) cc_final: 0.8778 (t0) REVERT: C 225 LYS cc_start: 0.8640 (mppt) cc_final: 0.8201 (mptt) REVERT: C 249 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7810 (tpt170) REVERT: C 370 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8351 (tt) REVERT: D 134 ASP cc_start: 0.8966 (t0) cc_final: 0.8709 (t0) REVERT: E 318 ARG cc_start: 0.7348 (mpt180) cc_final: 0.6879 (mmt-90) outliers start: 22 outliers final: 13 residues processed: 74 average time/residue: 0.5898 time to fit residues: 47.8293 Evaluate side-chains 72 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 361 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 149 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS E 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.072378 restraints weight = 28127.317| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.30 r_work: 0.2947 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12027 Z= 0.154 Angle : 0.480 7.511 16269 Z= 0.256 Chirality : 0.044 0.148 1814 Planarity : 0.003 0.037 2100 Dihedral : 4.277 49.705 1656 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.83 % Allowed : 14.35 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.22), residues: 1495 helix: 1.94 (0.24), residues: 455 sheet: 1.12 (0.30), residues: 306 loop : -0.07 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 192 TYR 0.014 0.001 TYR C 287 PHE 0.011 0.001 PHE D 385 TRP 0.018 0.001 TRP E 317 HIS 0.006 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00361 (12027) covalent geometry : angle 0.47978 (16269) hydrogen bonds : bond 0.03512 ( 529) hydrogen bonds : angle 4.01715 ( 1479) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8187 (mptp) REVERT: A 252 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8143 (tp) REVERT: B 189 MET cc_start: 0.8784 (ttp) cc_final: 0.7984 (tpp) REVERT: C 33 ILE cc_start: 0.8744 (mt) cc_final: 0.8506 (mt) REVERT: C 189 MET cc_start: 0.8225 (tpt) cc_final: 0.7907 (tpt) REVERT: C 192 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7829 (tpm170) REVERT: C 220 ASP cc_start: 0.9062 (t70) cc_final: 0.8752 (t0) REVERT: C 225 LYS cc_start: 0.8658 (mppt) cc_final: 0.8218 (mptt) REVERT: C 249 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7850 (tpt170) REVERT: C 370 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8413 (tt) REVERT: D 134 ASP cc_start: 0.8952 (t0) cc_final: 0.8730 (t0) REVERT: E 318 ARG cc_start: 0.7359 (mpt180) cc_final: 0.6904 (mmt-90) outliers start: 23 outliers final: 13 residues processed: 75 average time/residue: 0.5421 time to fit residues: 44.7764 Evaluate side-chains 73 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 110 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS E 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.072610 restraints weight = 27116.938| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.26 r_work: 0.2952 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12027 Z= 0.147 Angle : 0.480 7.401 16269 Z= 0.256 Chirality : 0.044 0.153 1814 Planarity : 0.003 0.036 2100 Dihedral : 4.282 51.836 1656 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.67 % Allowed : 14.59 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1495 helix: 1.94 (0.24), residues: 455 sheet: 1.13 (0.30), residues: 306 loop : -0.07 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 192 TYR 0.014 0.001 TYR B 287 PHE 0.010 0.001 PHE D 385 TRP 0.025 0.001 TRP E 317 HIS 0.007 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00344 (12027) covalent geometry : angle 0.48015 (16269) hydrogen bonds : bond 0.03449 ( 529) hydrogen bonds : angle 4.00579 ( 1479) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8178 (mptp) REVERT: A 192 ARG cc_start: 0.8024 (mmp80) cc_final: 0.7688 (mmp80) REVERT: A 252 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8145 (tp) REVERT: B 189 MET cc_start: 0.8783 (ttp) cc_final: 0.7989 (tpp) REVERT: C 33 ILE cc_start: 0.8729 (mt) cc_final: 0.8486 (mt) REVERT: C 189 MET cc_start: 0.8205 (tpt) cc_final: 0.7876 (tpt) REVERT: C 192 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7828 (tpm170) REVERT: C 220 ASP cc_start: 0.9075 (t70) cc_final: 0.8793 (t0) REVERT: C 225 LYS cc_start: 0.8672 (mppt) cc_final: 0.8241 (mptt) REVERT: C 370 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8407 (tt) REVERT: D 134 ASP cc_start: 0.8977 (t0) cc_final: 0.8746 (t0) REVERT: E 318 ARG cc_start: 0.7354 (mpt180) cc_final: 0.6918 (mmt-90) outliers start: 21 outliers final: 13 residues processed: 75 average time/residue: 0.5528 time to fit residues: 45.5438 Evaluate side-chains 72 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 38 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS E 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072938 restraints weight = 26634.340| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.22 r_work: 0.2961 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12027 Z= 0.131 Angle : 0.486 10.498 16269 Z= 0.260 Chirality : 0.044 0.151 1814 Planarity : 0.003 0.036 2100 Dihedral : 4.000 15.080 1652 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.52 % Allowed : 14.83 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.22), residues: 1495 helix: 1.94 (0.24), residues: 455 sheet: 1.13 (0.30), residues: 306 loop : -0.05 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 192 TYR 0.012 0.001 TYR D 271 PHE 0.009 0.001 PHE D 385 TRP 0.032 0.001 TRP E 317 HIS 0.008 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00307 (12027) covalent geometry : angle 0.48573 (16269) hydrogen bonds : bond 0.03353 ( 529) hydrogen bonds : angle 3.98111 ( 1479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3369.39 seconds wall clock time: 58 minutes 34.84 seconds (3514.84 seconds total)