Starting phenix.real_space_refine on Sun Oct 25 03:13:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hbz_52035/10_2026/9hbz_52035.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hbz_52035/10_2026/9hbz_52035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hbz_52035/10_2026/9hbz_52035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hbz_52035/10_2026/9hbz_52035.map" model { file = "/net/cci-nas-00/data/ceres_data/9hbz_52035/10_2026/9hbz_52035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hbz_52035/10_2026/9hbz_52035.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 102 5.16 5 C 9690 2.51 5 N 2829 2.21 5 O 3021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15706 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2392 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2418 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'RNA': 12} Modifications used: {'rna2p': 3, 'rna3p': 9} Link IDs: {'rna2p': 3, 'rna3p': 8} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2402 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'RNA': 10} Modifications used: {'rna2p': 2, 'rna3p': 8} Link IDs: {'rna2p': 2, 'rna3p': 7} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Chain: "E" Number of atoms: 2410 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 313, 2399 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 313, 2399 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2427 Chain: "H" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 198 Classifications: {'RNA': 10} Modifications used: {'rna2p': 1, 'rna3p': 9} Link IDs: {'rna2p': 1, 'rna3p': 8} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Chain: "G" Number of atoms: 2384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 309, 2373 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 309, 2373 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2401 Chain: "I" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'RNA': 12} Modifications used: {'rna2p': 2, 'rna3p': 10} Link IDs: {'rna2p': 2, 'rna3p': 9} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'RNA': 10} Modifications used: {'rna2p': 2, 'rna3p': 8} Link IDs: {'rna2p': 2, 'rna3p': 7} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Chain: "K" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 198 Classifications: {'RNA': 10} Modifications used: {'rna2p': 2, 'rna3p': 8} Link IDs: {'rna2p': 2, 'rna3p': 7} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG E 198 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG E 198 " occ=0.40 residue: pdb=" N AARG G 198 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG G 198 " occ=0.40 Time building chain proxies: 4.43, per 1000 atoms: 0.28 Number of scatterers: 15706 At special positions: 0 Unit cell: (138.918, 133.986, 84.666, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 P 64 15.00 O 3021 8.00 N 2829 7.00 C 9690 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: 0.92 Conformation dependent library (CDL) restraints added in 621.8 milliseconds 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3448 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 15 sheets defined 51.7% alpha, 5.7% beta 0 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.536A pdb=" N PHE A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 118 through 128 removed outlier: 4.481A pdb=" N GLU A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 143 through 173 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.522A pdb=" N LYS A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 249 through 258 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.681A pdb=" N LEU A 266 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'C' and resid 36 through 51 removed outlier: 3.518A pdb=" N PHE C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 58 through 74 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 134 through 142 Processing helix chain 'C' and resid 143 through 172 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 206 through 214 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.713A pdb=" N LEU C 266 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 3.641A pdb=" N GLU C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 312' Processing helix chain 'C' and resid 317 through 320 removed outlier: 3.652A pdb=" N GLU C 320 " --> pdb=" O ASN C 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 317 through 320' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 58 through 74 Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.656A pdb=" N VAL D 128 " --> pdb=" O CYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 Processing helix chain 'D' and resid 143 through 173 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 193 through 200 removed outlier: 3.507A pdb=" N CYS D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.707A pdb=" N LEU D 266 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 312 removed outlier: 3.668A pdb=" N GLU D 311 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 312' Processing helix chain 'D' and resid 317 through 320 removed outlier: 3.565A pdb=" N GLU D 320 " --> pdb=" O ASN D 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 320' Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'B' and resid 36 through 51 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 58 through 74 Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.700A pdb=" N VAL B 128 " --> pdb=" O CYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 143 through 173 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 206 through 214 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.532A pdb=" N LEU B 266 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'E' and resid 36 through 51 Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 58 through 74 Processing helix chain 'E' and resid 88 through 101 Processing helix chain 'E' and resid 119 through 128 removed outlier: 3.552A pdb=" N VAL E 128 " --> pdb=" O CYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 142 Processing helix chain 'E' and resid 143 through 175 removed outlier: 4.108A pdb=" N VAL E 174 " --> pdb=" O TYR E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 193 through 200 Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.720A pdb=" N ALA E 209 " --> pdb=" O GLY E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 239 removed outlier: 3.814A pdb=" N ILE E 238 " --> pdb=" O ARG E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.531A pdb=" N LEU E 266 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'G' and resid 36 through 51 Processing helix chain 'G' and resid 52 through 54 No H-bonds generated for 'chain 'G' and resid 52 through 54' Processing helix chain 'G' and resid 58 through 74 Processing helix chain 'G' and resid 88 through 101 removed outlier: 3.558A pdb=" N ARG G 94 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 removed outlier: 3.634A pdb=" N VAL G 128 " --> pdb=" O CYS G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 142 Processing helix chain 'G' and resid 143 through 175 removed outlier: 4.080A pdb=" N VAL G 174 " --> pdb=" O TYR G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 188 removed outlier: 4.097A pdb=" N TRP G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 200 Processing helix chain 'G' and resid 205 through 215 removed outlier: 3.519A pdb=" N ALA G 209 " --> pdb=" O GLY G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 317 through 320 removed outlier: 3.530A pdb=" N GLU G 320 " --> pdb=" O ASN G 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 317 through 320' Processing helix chain 'G' and resid 340 through 349 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA3, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AA4, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AA5, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA6, first strand: chain 'D' and resid 247 through 248 removed outlier: 7.552A pdb=" N ILE D 279 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 273 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 248 removed outlier: 3.531A pdb=" N VAL B 248 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 285 through 286 Processing sheet with id=AB1, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AB2, first strand: chain 'E' and resid 270 through 273 removed outlier: 3.977A pdb=" N SER E 273 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE E 279 " --> pdb=" O SER E 273 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AB4, first strand: chain 'G' and resid 109 through 110 Processing sheet with id=AB5, first strand: chain 'G' and resid 270 through 273 removed outlier: 3.854A pdb=" N SER G 273 " --> pdb=" O ILE G 279 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE G 279 " --> pdb=" O SER G 273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 284 through 286 658 hydrogen bonds defined for protein. 1907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.29 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: 4991 1.34 - 1.46: 3755 1.46 - 1.58: 7111 1.58 - 1.69: 122 1.69 - 1.81: 138 Bond restraints: 16117 Sorted by residual: bond pdb=" C2 Y5P F 12 " pdb=" N3 Y5P F 12 " ideal model delta sigma weight residual 1.268 1.373 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C2 Y5P O 12 " pdb=" N3 Y5P O 12 " ideal model delta sigma weight residual 1.268 1.373 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C2 Y5P I 412 " pdb=" N3 Y5P I 412 " ideal model delta sigma weight residual 1.268 1.373 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C2 Y5P F 8 " pdb=" N3 Y5P F 8 " ideal model delta sigma weight residual 1.268 1.373 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C2 Y5P H 10 " pdb=" N3 Y5P H 10 " ideal model delta sigma weight residual 1.268 1.373 -0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 16112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 21560 2.39 - 4.78: 277 4.78 - 7.17: 72 7.17 - 9.56: 22 9.56 - 11.95: 22 Bond angle restraints: 21953 Sorted by residual: angle pdb=" N1 Y5P K 407 " pdb=" C2 Y5P K 407 " pdb=" N3 Y5P K 407 " ideal model delta sigma weight residual 126.68 114.73 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N1 Y5P H 12 " pdb=" C2 Y5P H 12 " pdb=" N3 Y5P H 12 " ideal model delta sigma weight residual 126.68 114.74 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" N1 Y5P O 12 " pdb=" C2 Y5P O 12 " pdb=" N3 Y5P O 12 " ideal model delta sigma weight residual 126.68 114.78 11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N1 Y5P H 8 " pdb=" C2 Y5P H 8 " pdb=" N3 Y5P H 8 " ideal model delta sigma weight residual 126.68 114.81 11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N1 Y5P H 10 " pdb=" C2 Y5P H 10 " pdb=" N3 Y5P H 10 " ideal model delta sigma weight residual 126.68 114.83 11.85 3.00e+00 1.11e-01 1.56e+01 ... (remaining 21948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 9641 24.21 - 48.42: 755 48.42 - 72.64: 262 72.64 - 96.85: 137 96.85 - 121.06: 6 Dihedral angle restraints: 10801 sinusoidal: 5439 harmonic: 5362 Sorted by residual: dihedral pdb=" P Y5P K 407 " pdb=" O5' Y5P K 407 " pdb=" C5' Y5P K 407 " pdb=" C4' Y5P K 407 " ideal model delta sinusoidal sigma weight residual 248.90 127.84 121.06 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" P Y5P H 8 " pdb=" O5' Y5P H 8 " pdb=" C5' Y5P H 8 " pdb=" C4' Y5P H 8 " ideal model delta sinusoidal sigma weight residual 248.90 137.21 111.69 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" P Y5P I 408 " pdb=" O5' Y5P I 408 " pdb=" C5' Y5P I 408 " pdb=" C4' Y5P I 408 " ideal model delta sinusoidal sigma weight residual 248.90 142.67 106.23 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 10798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1693 0.028 - 0.055: 526 0.055 - 0.082: 120 0.082 - 0.110: 70 0.110 - 0.137: 51 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA ILE D 325 " pdb=" N ILE D 325 " pdb=" C ILE D 325 " pdb=" CB ILE D 325 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE C 230 " pdb=" N ILE C 230 " pdb=" C ILE C 230 " pdb=" CB ILE C 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE D 230 " pdb=" N ILE D 230 " pdb=" C ILE D 230 " pdb=" CB ILE D 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 2457 not shown) Planarity restraints: 2599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 35 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO E 36 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO E 36 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 36 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 35 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO D 36 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 189 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.30e+00 pdb=" N PRO A 190 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 190 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 190 " 0.014 5.00e-02 4.00e+02 ... (remaining 2596 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 107 2.54 - 3.13: 12085 3.13 - 3.72: 24655 3.72 - 4.31: 33618 4.31 - 4.90: 55955 Nonbonded interactions: 126420 Sorted by model distance: nonbonded pdb=" OG SER E 340 " pdb=" O LEU G 295 " model vdw 1.956 3.040 nonbonded pdb=" OG SER D 340 " pdb=" O LEU E 295 " model vdw 2.017 3.040 nonbonded pdb=" O GLY D 338 " pdb=" OG SER E 308 " model vdw 2.023 3.040 nonbonded pdb=" OE2 GLU C 321 " pdb=" OG SER D 303 " model vdw 2.105 3.040 nonbonded pdb=" NH1 ARG D 179 " pdb=" O ARG E 217 " model vdw 2.119 3.120 ... (remaining 126415 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 34 through 197 or resid 199 through 290 or resid 293 throu \ gh 310 or resid 317 through 349)) selection = (chain 'B' and (resid 34 through 197 or resid 199 through 290 or resid 293 throu \ gh 310 or resid 317 through 349)) selection = (chain 'C' and (resid 34 through 197 or resid 199 through 290 or resid 293 throu \ gh 310 or resid 317 through 349)) selection = (chain 'D' and (resid 34 through 197 or resid 199 through 290 or resid 293 throu \ gh 310 or resid 317 through 349)) selection = (chain 'E' and (resid 34 through 197 or resid 199 through 290 or resid 293 throu \ gh 310 or resid 317 through 349)) selection = (chain 'G' and (resid 34 through 197 or resid 199 through 349)) } ncs_group { reference = (chain 'F' and (resid 4 through 7 or resid 9)) selection = (chain 'H' and (resid 4 through 7 or resid 9)) selection = (chain 'J' and (resid 402 through 405 or resid 407)) selection = (chain 'K' and (resid 402 through 405 or resid 407)) } ncs_group { reference = chain 'I' selection = chain 'O' } 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=0.40 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: 3.980 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.800 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 16117 Z= 0.395 Angle : 0.829 11.951 21953 Z= 0.343 Chirality : 0.035 0.137 2460 Planarity : 0.003 0.032 2599 Dihedral : 21.206 121.061 7353 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.23 % Allowed : 18.03 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.36 (0.21), residues: 1861 helix: 1.79 (0.18), residues: 882 sheet: -1.18 (0.50), residues: 76 loop : 0.31 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 309 TYR 0.009 0.001 TYR D 197 PHE 0.008 0.001 PHE C 235 TRP 0.009 0.001 TRP C 259 HIS 0.005 0.001 HIS E 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00791 / 0.39 (16117) covalent geometry : angle 0.82930 / 0.34 (21953) hydrogen bonds : bond 0.12879 / 8.57 ( 658) hydrogen bonds : angle 5.12250 / 3.70 ( 1907) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 425 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 THR cc_start: 0.6360 (p) cc_final: 0.5941 (m) REVERT: C 283 VAL cc_start: 0.8569 (m) cc_final: 0.8301 (t) REVERT: D 221 TYR cc_start: 0.7487 (t80) cc_final: 0.6968 (t80) REVERT: B 135 MET cc_start: 0.0272 (tpt) cc_final: 0.0025 (tpt) REVERT: E 50 PHE cc_start: 0.3306 (m-80) cc_final: 0.2662 (m-10) REVERT: E 70 PHE cc_start: 0.6342 (t80) cc_final: 0.5946 (t80) REVERT: E 161 VAL cc_start: 0.8033 (t) cc_final: 0.7616 (p) outliers start: 32 outliers final: 14 residues processed: 454 average time/residue: 0.1556 time to fit residues: 97.0608 Evaluate side-chains 236 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain G residue 155 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 317 ASN C 240 HIS D 96 ASN D 240 HIS ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 181 GLN B 240 HIS B 243 GLN E 38 ASN G 96 ASN G 153 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.265734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.228981 restraints weight = 38118.576| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 4.06 r_work (final): 0.4703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4703 r_free = 0.4703 target_work(ls_wunit_k1) = 0.227 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4702 r_free = 0.4702 target_work(ls_wunit_k1) = 0.227 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.4702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 16117 Z= 0.311 Angle : 0.804 13.918 21953 Z= 0.404 Chirality : 0.045 0.182 2460 Planarity : 0.006 0.057 2599 Dihedral : 22.228 120.027 3938 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.87 % Allowed : 22.62 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.41 (0.20), residues: 1861 helix: 0.81 (0.17), residues: 892 sheet: -1.28 (0.50), residues: 78 loop : -0.01 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 158 TYR 0.025 0.003 TYR G 123 PHE 0.025 0.003 PHE D 70 TRP 0.037 0.003 TRP E 120 HIS 0.014 0.002 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.31 (16117) covalent geometry : angle 0.80367 / 0.40 (21953) hydrogen bonds : bond 0.04755 / 3.20 ( 658) hydrogen bonds : angle 4.86799 / 3.57 ( 1907) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.5173 (pt0) REVERT: C 241 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6649 (tpt170) REVERT: C 283 VAL cc_start: 0.8708 (m) cc_final: 0.8391 (t) REVERT: D 198 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7874 (ttm-80) REVERT: B 136 LYS cc_start: 0.1791 (OUTLIER) cc_final: 0.0592 (mptt) REVERT: B 149 MET cc_start: 0.1287 (tmm) cc_final: 0.1075 (tmm) REVERT: B 243 GLN cc_start: 0.1957 (OUTLIER) cc_final: 0.1173 (pm20) REVERT: G 135 MET cc_start: 0.2406 (mtm) cc_final: 0.2176 (mtp) outliers start: 57 outliers final: 25 residues processed: 292 average time/residue: 0.1314 time to fit residues: 55.7231 Evaluate side-chains 229 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 257 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [144, 145, 131, 18, 165, 102, 156, 66, 31, 11, 184] chunk 144 optimal weight: 5.9990 chunk 145 optimal weight: 0.0000 chunk 131 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 165 optimal weight: 40.0000 chunk 102 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 181 GLN B 240 HIS B 243 GLN E 226 GLN ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.267216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.232926 restraints weight = 48225.864| |-----------------------------------------------------------------------------| r_work (start): 0.4743 rms_B_bonded: 4.26 r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4743 r_free = 0.4743 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4743 r_free = 0.4743 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16117 Z= 0.173 Angle : 0.682 14.280 21953 Z= 0.340 Chirality : 0.040 0.177 2460 Planarity : 0.005 0.072 2599 Dihedral : 21.820 118.153 3927 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.28 % Allowed : 24.07 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.39 (0.20), residues: 1861 helix: 0.80 (0.17), residues: 901 sheet: -1.30 (0.51), residues: 78 loop : -0.02 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 158 TYR 0.021 0.002 TYR E 123 PHE 0.020 0.002 PHE B 70 TRP 0.036 0.002 TRP E 120 HIS 0.015 0.002 HIS E 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (16117) covalent geometry : angle 0.68187 / 0.34 (21953) hydrogen bonds : bond 0.03995 / 2.71 ( 658) hydrogen bonds : angle 4.59372 / 3.39 ( 1907) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 241 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6538 (tpt170) REVERT: C 283 VAL cc_start: 0.8664 (m) cc_final: 0.8319 (t) REVERT: D 116 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7492 (mp) REVERT: B 136 LYS cc_start: 0.1764 (OUTLIER) cc_final: 0.0547 (mptt) outliers start: 48 outliers final: 25 residues processed: 274 average time/residue: 0.1283 time to fit residues: 51.3863 Evaluate side-chains 232 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain G residue 153 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [10, 66, 85, 167, 81, 5, 133, 46, 17, 139, 121] chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 0.0570 chunk 133 optimal weight: 0.0870 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 181 GLN B 243 GLN E 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.268950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.234719 restraints weight = 44558.599| |-----------------------------------------------------------------------------| r_work (start): 0.4755 rms_B_bonded: 4.00 r_work (final): 0.4755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4756 r_free = 0.4756 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4756 r_free = 0.4756 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16117 Z= 0.124 Angle : 0.656 13.271 21953 Z= 0.324 Chirality : 0.039 0.173 2460 Planarity : 0.004 0.047 2599 Dihedral : 21.619 118.784 3925 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.21 % Allowed : 23.87 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.53 (0.20), residues: 1861 helix: 0.97 (0.18), residues: 901 sheet: -1.26 (0.51), residues: 78 loop : -0.01 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 86 TYR 0.030 0.002 TYR G 170 PHE 0.021 0.002 PHE B 50 TRP 0.020 0.002 TRP E 120 HIS 0.015 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (16117) covalent geometry : angle 0.65580 / 0.32 (21953) hydrogen bonds : bond 0.03644 / 2.46 ( 658) hydrogen bonds : angle 4.40304 / 3.26 ( 1907) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6421 (mmp) cc_final: 0.6182 (mmp) REVERT: C 158 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7669 (ttm110) REVERT: C 283 VAL cc_start: 0.8639 (m) cc_final: 0.8273 (t) REVERT: D 116 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7456 (mp) REVERT: D 198 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7589 (ttm-80) REVERT: B 136 LYS cc_start: 0.2020 (OUTLIER) cc_final: 0.0586 (mptt) REVERT: B 243 GLN cc_start: 0.1152 (OUTLIER) cc_final: 0.0676 (tt0) REVERT: E 183 LEU cc_start: 0.6229 (mt) cc_final: 0.5837 (mt) REVERT: E 326 GLN cc_start: 0.5141 (tm-30) cc_final: 0.4803 (tm-30) REVERT: G 259 TRP cc_start: 0.4529 (p-90) cc_final: 0.4177 (p-90) outliers start: 47 outliers final: 26 residues processed: 260 average time/residue: 0.1294 time to fit residues: 49.1965 Evaluate side-chains 238 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain G residue 153 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [2, 172, 156, 47, 126, 66, 74, 139, 1, 10, 43] chunk 2 optimal weight: 0.9980 chunk 172 optimal weight: 30.0000 chunk 156 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 288 GLN B 154 ASN B 243 GLN G 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.268290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.238195 restraints weight = 49887.156| |-----------------------------------------------------------------------------| r_work (start): 0.4788 rms_B_bonded: 3.78 r_work: 0.4456 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4431 r_free = 0.4431 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4431 r_free = 0.4431 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16117 Z= 0.145 Angle : 0.671 12.964 21953 Z= 0.331 Chirality : 0.040 0.211 2460 Planarity : 0.004 0.043 2599 Dihedral : 21.446 121.871 3924 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.41 % Allowed : 24.26 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.47 (0.20), residues: 1861 helix: 0.92 (0.18), residues: 902 sheet: -1.32 (0.50), residues: 78 loop : -0.04 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 86 TYR 0.034 0.002 TYR E 170 PHE 0.023 0.002 PHE B 70 TRP 0.026 0.002 TRP E 120 HIS 0.010 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (16117) covalent geometry : angle 0.67091 / 0.33 (21953) hydrogen bonds : bond 0.03642 / 2.46 ( 658) hydrogen bonds : angle 4.39094 / 3.24 ( 1907) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 VAL cc_start: 0.6221 (OUTLIER) cc_final: 0.5687 (m) REVERT: A 334 CYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6934 (m) REVERT: C 149 MET cc_start: 0.6389 (tmm) cc_final: 0.6030 (ttp) REVERT: C 158 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7668 (ttm110) REVERT: C 219 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7583 (pttm) REVERT: C 283 VAL cc_start: 0.8595 (m) cc_final: 0.8252 (t) REVERT: D 116 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7690 (mp) REVERT: D 313 THR cc_start: 0.6239 (OUTLIER) cc_final: 0.5557 (t) REVERT: B 136 LYS cc_start: 0.1978 (OUTLIER) cc_final: 0.0538 (mptt) REVERT: E 183 LEU cc_start: 0.7067 (mt) cc_final: 0.6775 (mt) REVERT: E 326 GLN cc_start: 0.5533 (tm-30) cc_final: 0.5141 (tm-30) REVERT: G 259 TRP cc_start: 0.5010 (p-90) cc_final: 0.4582 (p-90) outliers start: 50 outliers final: 36 residues processed: 250 average time/residue: 0.1288 time to fit residues: 47.1481 Evaluate side-chains 243 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain G residue 207 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [144, 75, 114, 90, 113, 122, 130, 136, 1, 27, 162] chunk 144 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 162 optimal weight: 30.0000 overall best weight: 1.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN E 187 GLN E 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.266697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.236878 restraints weight = 50558.117| |-----------------------------------------------------------------------------| r_work (start): 0.4778 rms_B_bonded: 3.73 r_work: 0.4478 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4463 r_free = 0.4463 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4463 r_free = 0.4463 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16117 Z= 0.184 Angle : 0.685 12.531 21953 Z= 0.338 Chirality : 0.041 0.290 2460 Planarity : 0.004 0.059 2599 Dihedral : 21.311 115.426 3924 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.93 % Allowed : 24.13 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.40 (0.20), residues: 1861 helix: 0.84 (0.17), residues: 898 sheet: -1.24 (0.50), residues: 76 loop : -0.07 (0.22), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 101 TYR 0.039 0.002 TYR E 170 PHE 0.031 0.002 PHE B 50 TRP 0.031 0.002 TRP B 188 HIS 0.006 0.001 HIS E 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (16117) covalent geometry : angle 0.68459 / 0.34 (21953) hydrogen bonds : bond 0.03728 / 2.50 ( 658) hydrogen bonds : angle 4.44093 / 3.29 ( 1907) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6393 (mmp) cc_final: 0.6053 (mmp) REVERT: A 296 VAL cc_start: 0.5969 (OUTLIER) cc_final: 0.5432 (m) REVERT: A 334 CYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6956 (m) REVERT: C 241 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6621 (tpt170) REVERT: C 283 VAL cc_start: 0.8639 (m) cc_final: 0.8337 (t) REVERT: D 116 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7590 (mp) REVERT: D 313 THR cc_start: 0.6349 (OUTLIER) cc_final: 0.5697 (t) REVERT: B 136 LYS cc_start: 0.2058 (OUTLIER) cc_final: 0.0568 (mptt) REVERT: B 243 GLN cc_start: 0.1333 (OUTLIER) cc_final: 0.0779 (tt0) REVERT: E 326 GLN cc_start: 0.5411 (tm-30) cc_final: 0.5020 (tm-30) REVERT: G 167 LYS cc_start: 0.5293 (tppt) cc_final: 0.4922 (tttt) outliers start: 58 outliers final: 40 residues processed: 250 average time/residue: 0.1200 time to fit residues: 44.3031 Evaluate side-chains 240 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain G residue 207 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [77, 25, 90, 112, 30, 153, 187, 87, 17, 143, 48] chunk 77 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 112 optimal weight: 0.0040 chunk 30 optimal weight: 0.9990 chunk 153 optimal weight: 0.0770 chunk 187 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 226 GLN E 187 GLN E 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.269483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.239486 restraints weight = 45990.841| |-----------------------------------------------------------------------------| r_work (start): 0.4803 rms_B_bonded: 3.70 r_work: 0.4464 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4438 r_free = 0.4438 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4438 r_free = 0.4438 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16117 Z= 0.113 Angle : 0.650 13.262 21953 Z= 0.318 Chirality : 0.039 0.219 2460 Planarity : 0.004 0.041 2599 Dihedral : 21.157 116.349 3924 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.75 % Allowed : 25.64 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.54 (0.20), residues: 1861 helix: 0.97 (0.18), residues: 901 sheet: -1.16 (0.52), residues: 78 loop : -0.02 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 86 TYR 0.050 0.002 TYR E 170 PHE 0.027 0.002 PHE B 50 TRP 0.036 0.002 TRP B 188 HIS 0.014 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16117) covalent geometry : angle 0.64960 / 0.32 (21953) hydrogen bonds : bond 0.03391 / 2.29 ( 658) hydrogen bonds : angle 4.33306 / 3.20 ( 1907) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 VAL cc_start: 0.6070 (OUTLIER) cc_final: 0.5573 (m) REVERT: A 334 CYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6885 (m) REVERT: C 283 VAL cc_start: 0.8537 (m) cc_final: 0.8191 (t) REVERT: D 116 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7673 (mp) REVERT: D 313 THR cc_start: 0.6340 (OUTLIER) cc_final: 0.5665 (t) REVERT: B 136 LYS cc_start: 0.1847 (OUTLIER) cc_final: 0.0427 (mptt) REVERT: E 326 GLN cc_start: 0.5634 (tm-30) cc_final: 0.5229 (tm-30) REVERT: G 72 MET cc_start: 0.4633 (OUTLIER) cc_final: 0.3534 (tmm) outliers start: 40 outliers final: 28 residues processed: 224 average time/residue: 0.1272 time to fit residues: 42.3419 Evaluate side-chains 222 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain G residue 207 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [93, 38, 136, 115, 171, 41, 161, 5, 21, 160, 48] chunk 93 optimal weight: 20.0000 chunk 38 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 171 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 5 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.268209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.240004 restraints weight = 40038.351| |-----------------------------------------------------------------------------| r_work (start): 0.4809 rms_B_bonded: 3.34 r_work: 0.4501 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4476 r_free = 0.4476 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4476 r_free = 0.4476 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16117 Z= 0.141 Angle : 0.663 12.591 21953 Z= 0.323 Chirality : 0.041 0.496 2460 Planarity : 0.004 0.052 2599 Dihedral : 21.049 117.481 3924 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.21 % Allowed : 25.25 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.46 (0.20), residues: 1861 helix: 0.90 (0.18), residues: 900 sheet: -1.13 (0.52), residues: 78 loop : -0.06 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 86 TYR 0.047 0.002 TYR E 170 PHE 0.025 0.002 PHE B 50 TRP 0.078 0.002 TRP G 188 HIS 0.010 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (16117) covalent geometry : angle 0.66341 / 0.32 (21953) hydrogen bonds : bond 0.03445 / 2.33 ( 658) hydrogen bonds : angle 4.34147 / 3.20 ( 1907) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6447 (mmp) cc_final: 0.6112 (mmp) REVERT: A 296 VAL cc_start: 0.6006 (OUTLIER) cc_final: 0.5457 (m) REVERT: A 334 CYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6994 (m) REVERT: C 241 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6566 (tpt170) REVERT: C 283 VAL cc_start: 0.8574 (m) cc_final: 0.8255 (t) REVERT: D 313 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.5653 (t) REVERT: B 108 MET cc_start: 0.4056 (tpp) cc_final: 0.3093 (mtp) REVERT: B 136 LYS cc_start: 0.2008 (OUTLIER) cc_final: 0.0575 (mptt) REVERT: B 243 GLN cc_start: 0.0976 (pm20) cc_final: 0.0720 (pm20) REVERT: E 326 GLN cc_start: 0.5438 (tm-30) cc_final: 0.5051 (tm-30) REVERT: G 72 MET cc_start: 0.4693 (OUTLIER) cc_final: 0.3633 (tmm) outliers start: 47 outliers final: 31 residues processed: 222 average time/residue: 0.1257 time to fit residues: 41.4168 Evaluate side-chains 222 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain G residue 207 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [0, 147, 7, 158, 73, 168, 103, 183, 71, 40, 172] chunk 0 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 158 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS E 187 GLN E 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.264606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.232815 restraints weight = 57081.558| |-----------------------------------------------------------------------------| r_work (start): 0.4745 rms_B_bonded: 4.22 r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4746 r_free = 0.4746 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4746 r_free = 0.4746 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 16117 Z= 0.239 Angle : 0.755 11.834 21953 Z= 0.375 Chirality : 0.046 0.498 2460 Planarity : 0.005 0.060 2599 Dihedral : 21.009 118.465 3924 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.15 % Allowed : 25.70 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.04 (0.20), residues: 1861 helix: 0.51 (0.17), residues: 898 sheet: -1.30 (0.51), residues: 80 loop : -0.21 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 86 TYR 0.038 0.003 TYR E 170 PHE 0.045 0.003 PHE A 50 TRP 0.082 0.003 TRP G 188 HIS 0.015 0.002 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 (16117) covalent geometry : angle 0.75467 / 0.38 (21953) hydrogen bonds : bond 0.04029 / 2.69 ( 658) hydrogen bonds : angle 4.65162 / 3.42 ( 1907) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 MET cc_start: 0.7079 (tmm) cc_final: 0.6755 (ttp) REVERT: C 158 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7807 (ttm110) REVERT: C 241 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6230 (tpt170) REVERT: C 283 VAL cc_start: 0.8763 (m) cc_final: 0.8510 (t) REVERT: D 116 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7508 (mp) REVERT: B 136 LYS cc_start: 0.2095 (OUTLIER) cc_final: 0.0671 (mptt) REVERT: E 326 GLN cc_start: 0.5291 (tm-30) cc_final: 0.5047 (tm-30) REVERT: G 72 MET cc_start: 0.4764 (OUTLIER) cc_final: 0.3832 (tmm) outliers start: 46 outliers final: 33 residues processed: 229 average time/residue: 0.1273 time to fit residues: 43.0959 Evaluate side-chains 222 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 259 TRP Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain G residue 189 PHE Chi-restraints excluded: chain G residue 207 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [123, 49, 44, 190, 24, 42, 82, 75, 159, 95, 186] chunk 123 optimal weight: 8.9990 chunk 49 optimal weight: 0.0070 chunk 44 optimal weight: 0.7980 chunk 190 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 159 optimal weight: 20.0000 chunk 95 optimal weight: 0.0000 chunk 186 optimal weight: 9.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN E 187 GLN E 343 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.268090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.239229 restraints weight = 38055.194| |-----------------------------------------------------------------------------| r_work (start): 0.4801 rms_B_bonded: 3.12 r_work: 0.4467 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4439 r_free = 0.4439 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4439 r_free = 0.4439 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16117 Z= 0.123 Angle : 0.707 14.711 21953 Z= 0.345 Chirality : 0.042 0.576 2460 Planarity : 0.004 0.066 2599 Dihedral : 20.837 119.069 3924 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.30 % Allowed : 26.95 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.20 (0.20), residues: 1861 helix: 0.68 (0.17), residues: 899 sheet: -1.31 (0.49), residues: 88 loop : -0.17 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 86 TYR 0.039 0.002 TYR E 170 PHE 0.030 0.002 PHE A 50 TRP 0.040 0.002 TRP G 188 HIS 0.014 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (16117) covalent geometry : angle 0.70713 / 0.35 (21953) hydrogen bonds : bond 0.03543 / 2.39 ( 658) hydrogen bonds : angle 4.50193 / 3.33 ( 1907) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 MET cc_start: 0.6701 (tmm) cc_final: 0.6151 (ttp) REVERT: C 283 VAL cc_start: 0.8569 (m) cc_final: 0.8245 (t) REVERT: D 58 ASP cc_start: 0.4757 (t70) cc_final: 0.4540 (t70) REVERT: D 116 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7600 (mp) REVERT: B 108 MET cc_start: 0.3990 (tpp) cc_final: 0.3207 (ttp) REVERT: B 136 LYS cc_start: 0.2010 (OUTLIER) cc_final: 0.0649 (mptt) REVERT: E 72 MET cc_start: 0.7146 (ppp) cc_final: 0.6803 (ppp) REVERT: E 326 GLN cc_start: 0.5654 (tm-30) cc_final: 0.5259 (tm-30) REVERT: G 72 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.3915 (tmm) REVERT: G 167 LYS cc_start: 0.5896 (tppt) cc_final: 0.5689 (tmtt) outliers start: 33 outliers final: 26 residues processed: 217 average time/residue: 0.1246 time to fit residues: 40.3587 Evaluate side-chains 215 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 120 TRP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 153 HIS Chi-restraints excluded: chain G residue 207 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: [114, 30, 77, 126, 145, 115, 9, 134, 65, 63, 122] chunk 114 optimal weight: 0.0010 chunk 30 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 126 optimal weight: 30.0000 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN E 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.268148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.236771 restraints weight = 58490.480| |-----------------------------------------------------------------------------| r_work (start): 0.4780 rms_B_bonded: 4.12 r_work (final): 0.4780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4779 r_free = 0.4779 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4779 r_free = 0.4779 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 16117 Z= 0.192 Angle : 0.897 59.200 21953 Z= 0.482 Chirality : 0.051 1.464 2460 Planarity : 0.004 0.039 2599 Dihedral : 20.836 119.074 3924 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.16 % Allowed : 27.21 % Favored : 70.62 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 10.00 % 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: 0.20 (0.20), residues: 1861 helix: 0.69 (0.17), residues: 899 sheet: -1.31 (0.49), residues: 88 loop : -0.17 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 86 TYR 0.038 0.002 TYR E 170 PHE 0.029 0.002 PHE B 50 TRP 0.035 0.002 TRP G 188 HIS 0.013 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (16117) covalent geometry : angle 0.89676 / 0.48 (21953) hydrogen bonds : bond 0.03563 / 2.40 ( 658) hydrogen bonds : angle 4.50319 / 3.33 ( 1907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.87 seconds wall clock time: 55 minutes 26.88 seconds (3326.88 seconds total)