Starting phenix.real_space_refine on Mon Jul 6 05:22:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxc_19573/07_2026/8rxc_19573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxc_19573/07_2026/8rxc_19573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rxc_19573/07_2026/8rxc_19573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxc_19573/07_2026/8rxc_19573.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxc_19573/07_2026/8rxc_19573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxc_19573/07_2026/8rxc_19573.cif" } resolution = 3.15 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16082 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 57 5.49 5 Mg 5 5.21 5 S 76 5.16 5 C 11946 2.51 5 N 3301 2.21 5 O 3821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19206 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3049 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 384} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3055 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain: "B" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3039 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain: "A" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3039 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain: "F" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2965 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain: "E" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3039 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 440 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 420 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.46, per 1000 atoms: 0.23 Number of scatterers: 19206 At special positions: 0 Unit cell: (119.915, 113.299, 120.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 57 15.00 Mg 5 11.99 O 3821 8.00 N 3301 7.00 C 11946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 838.1 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 20 sheets defined 36.2% alpha, 19.9% beta 7 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'D' and resid 74 through 81 removed outlier: 3.994A pdb=" N VAL D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 114 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 186 through 205 removed outlier: 3.693A pdb=" N GLU D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 230 removed outlier: 4.007A pdb=" N GLU D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 342 Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 366 through 380 Processing helix chain 'D' and resid 404 through 415 Processing helix chain 'D' and resid 425 through 428 removed outlier: 4.143A pdb=" N THR D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 428' Processing helix chain 'D' and resid 443 through 452 Processing helix chain 'C' and resid 74 through 82 removed outlier: 3.519A pdb=" N VAL C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.614A pdb=" N GLN C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.560A pdb=" N GLU C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 186 through 205 Processing helix chain 'C' and resid 223 through 230 removed outlier: 4.129A pdb=" N GLU C 227 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.914A pdb=" N PHE C 280 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 342 Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 380 Processing helix chain 'C' and resid 404 through 415 Processing helix chain 'C' and resid 425 through 428 removed outlier: 3.779A pdb=" N THR C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 428' Processing helix chain 'C' and resid 443 through 452 Processing helix chain 'B' and resid 59 through 63 removed outlier: 4.556A pdb=" N THR B 63 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.592A pdb=" N VAL B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 116 removed outlier: 3.759A pdb=" N VAL B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 151 through 163 Processing helix chain 'B' and resid 190 through 205 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 327 through 343 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 366 through 380 Processing helix chain 'B' and resid 404 through 415 Processing helix chain 'B' and resid 425 through 428 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.579A pdb=" N LEU A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.647A pdb=" N GLU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.516A pdb=" N HIS A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 380 Processing helix chain 'A' and resid 404 through 415 removed outlier: 3.510A pdb=" N ARG A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'F' and resid 74 through 81 Processing helix chain 'F' and resid 100 through 114 removed outlier: 3.721A pdb=" N GLN F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 151 through 161 removed outlier: 3.523A pdb=" N GLU F 160 " --> pdb=" O ARG F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 175 Processing helix chain 'F' and resid 186 through 205 Processing helix chain 'F' and resid 222 through 231 removed outlier: 4.016A pdb=" N LEU F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET F 229 " --> pdb=" O MET F 225 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 341 Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 363 through 365 No H-bonds generated for 'chain 'F' and resid 363 through 365' Processing helix chain 'F' and resid 366 through 380 Processing helix chain 'F' and resid 404 through 415 Processing helix chain 'F' and resid 443 through 452 Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 100 through 113 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.427A pdb=" N SER E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 186 through 205 Processing helix chain 'E' and resid 224 through 230 removed outlier: 3.731A pdb=" N HIS E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 342 Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 363 through 365 No H-bonds generated for 'chain 'E' and resid 363 through 365' Processing helix chain 'E' and resid 366 through 380 Processing helix chain 'E' and resid 404 through 415 Processing helix chain 'E' and resid 425 through 428 Processing helix chain 'E' and resid 443 through 452 Processing sheet with id=AA1, first strand: chain 'D' and resid 58 through 59 removed outlier: 6.576A pdb=" N LEU E 119 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL E 91 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU E 90 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU E 234 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU E 92 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE E 236 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY E 94 " --> pdb=" O PHE E 236 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLY E 238 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL E 233 " --> pdb=" O VAL E 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 269 through 272 removed outlier: 6.760A pdb=" N VAL D 233 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU D 90 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU D 234 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU D 92 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE D 236 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY D 94 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY D 95 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 167 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL D 211 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE D 169 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 170 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 349 through 355 removed outlier: 9.969A pdb=" N SER D 291 " --> pdb=" O GLU D 387 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N PHE D 389 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 293 " --> pdb=" O PHE D 389 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE D 420 " --> pdb=" O ILE D 439 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL D 441 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL D 422 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 392 through 393 removed outlier: 3.579A pdb=" N GLU D 392 " --> pdb=" O ARG D 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.194A pdb=" N VAL C 118 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N TYR C 147 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR C 120 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 119 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL C 91 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY C 212 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 93 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 90 " --> pdb=" O THR C 232 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU C 234 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 92 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE C 236 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY C 94 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 233 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 291 through 298 removed outlier: 6.666A pdb=" N THR C 322 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N SER C 355 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR C 324 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 387 through 389 removed outlier: 6.743A pdb=" N CYS C 388 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 420 " --> pdb=" O ILE C 439 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL C 441 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL C 422 " --> pdb=" O VAL C 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 392 through 393 Processing sheet with id=AA9, first strand: chain 'B' and resid 144 through 147 removed outlier: 6.359A pdb=" N VAL B 118 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR B 147 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR B 120 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 167 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL B 211 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 90 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU B 234 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 92 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE B 236 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY B 94 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLY B 238 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 233 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 323 through 324 removed outlier: 9.595A pdb=" N SER B 291 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N PHE B 389 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 293 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B 420 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL B 441 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL B 422 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 392 through 393 Processing sheet with id=AB3, first strand: chain 'A' and resid 144 through 147 removed outlier: 6.610A pdb=" N LEU A 167 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL A 211 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE A 169 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 90 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU A 234 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 92 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE A 236 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 94 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 233 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 291 through 298 Processing sheet with id=AB5, first strand: chain 'A' and resid 387 through 389 removed outlier: 6.758A pdb=" N CYS A 388 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 420 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL A 441 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 422 " --> pdb=" O VAL A 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 392 through 393 removed outlier: 3.711A pdb=" N GLU A 392 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.525A pdb=" N VAL F 118 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N TYR F 147 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR F 120 " --> pdb=" O TYR F 147 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU F 167 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL F 211 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE F 169 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL F 91 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY F 212 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE F 93 " --> pdb=" O GLY F 212 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU F 90 " --> pdb=" O THR F 232 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N LEU F 234 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 92 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE F 236 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY F 94 " --> pdb=" O PHE F 236 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL F 233 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU F 259 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 323 through 324 removed outlier: 3.710A pdb=" N ARG F 301 " --> pdb=" O GLU F 298 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N SER F 291 " --> pdb=" O GLU F 387 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N PHE F 389 " --> pdb=" O SER F 291 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE F 293 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS F 388 " --> pdb=" O TYR F 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 392 through 393 removed outlier: 3.877A pdb=" N GLU F 392 " --> pdb=" O ARG F 400 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 323 through 324 removed outlier: 9.641A pdb=" N SER E 291 " --> pdb=" O GLU E 387 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N PHE E 389 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE E 293 " --> pdb=" O PHE E 389 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS E 388 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 392 through 393 removed outlier: 3.577A pdb=" N GLU E 392 " --> pdb=" O ARG E 400 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6416 1.36 - 1.50: 4681 1.50 - 1.64: 8268 1.64 - 1.78: 52 1.78 - 1.93: 123 Bond restraints: 19540 Sorted by residual: bond pdb=" C3' AGS E 501 " pdb=" C4' AGS E 501 " ideal model delta sigma weight residual 1.530 1.312 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C3' AGS D 501 " pdb=" C4' AGS D 501 " ideal model delta sigma weight residual 1.530 1.314 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C3' AGS F 501 " pdb=" C4' AGS F 501 " ideal model delta sigma weight residual 1.530 1.319 0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3' AGS B 502 " pdb=" C4' AGS B 502 " ideal model delta sigma weight residual 1.530 1.319 0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3' AGS C 501 " pdb=" C4' AGS C 501 " ideal model delta sigma weight residual 1.530 1.321 0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 19535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 26404 3.59 - 7.19: 167 7.19 - 10.78: 30 10.78 - 14.37: 20 14.37 - 17.96: 15 Bond angle restraints: 26636 Sorted by residual: angle pdb=" N1 AGS E 501 " pdb=" C6 AGS E 501 " pdb=" N6 AGS E 501 " ideal model delta sigma weight residual 119.19 101.23 17.96 3.00e+00 1.11e-01 3.59e+01 angle pdb=" N1 AGS C 501 " pdb=" C6 AGS C 501 " pdb=" N6 AGS C 501 " ideal model delta sigma weight residual 119.19 101.49 17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" N1 AGS D 501 " pdb=" C6 AGS D 501 " pdb=" N6 AGS D 501 " ideal model delta sigma weight residual 119.19 101.49 17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" N1 AGS B 502 " pdb=" C6 AGS B 502 " pdb=" N6 AGS B 502 " ideal model delta sigma weight residual 119.19 101.56 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" N1 AGS F 501 " pdb=" C6 AGS F 501 " pdb=" N6 AGS F 501 " ideal model delta sigma weight residual 119.19 101.61 17.58 3.00e+00 1.11e-01 3.44e+01 ... (remaining 26631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 11329 35.47 - 70.93: 558 70.93 - 106.40: 60 106.40 - 141.87: 6 141.87 - 177.33: 8 Dihedral angle restraints: 11961 sinusoidal: 5217 harmonic: 6744 Sorted by residual: dihedral pdb=" CA ILE D 180 " pdb=" C ILE D 180 " pdb=" N SER D 181 " pdb=" CA SER D 181 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PHE F 280 " pdb=" C PHE F 280 " pdb=" N LEU F 281 " pdb=" CA LEU F 281 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PHE A 280 " pdb=" C PHE A 280 " pdb=" N LEU A 281 " pdb=" CA LEU A 281 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 11958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2321 0.048 - 0.097: 658 0.097 - 0.145: 194 0.145 - 0.194: 9 0.194 - 0.242: 3 Chirality restraints: 3185 Sorted by residual: chirality pdb=" CB ILE B 168 " pdb=" CA ILE B 168 " pdb=" CG1 ILE B 168 " pdb=" CG2 ILE B 168 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LEU D 415 " pdb=" N LEU D 415 " pdb=" C LEU D 415 " pdb=" CB LEU D 415 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE B 180 " pdb=" CA ILE B 180 " pdb=" CG1 ILE B 180 " pdb=" CG2 ILE B 180 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3182 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 191 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C ARG B 191 " 0.068 2.00e-02 2.50e+03 pdb=" O ARG B 191 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU B 192 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 96 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO A 97 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 380 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C ASP C 380 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP C 380 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS C 381 " 0.014 2.00e-02 2.50e+03 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 121 2.50 - 3.10: 14050 3.10 - 3.70: 28688 3.70 - 4.30: 42995 4.30 - 4.90: 70689 Nonbonded interactions: 156543 Sorted by model distance: nonbonded pdb=" OG SER E 102 " pdb="MG MG E 502 " model vdw 1.903 2.170 nonbonded pdb=" OG SER D 102 " pdb="MG MG D 502 " model vdw 1.917 2.170 nonbonded pdb=" O2G AGS D 501 " pdb="MG MG D 502 " model vdw 1.972 2.170 nonbonded pdb=" OG SER F 102 " pdb="MG MG F 502 " model vdw 1.978 2.170 nonbonded pdb=" O3G AGS D 501 " pdb="MG MG D 502 " model vdw 1.987 2.170 ... (remaining 156538 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 66 through 452) selection = (chain 'B' and resid 66 through 452) selection = (chain 'C' and resid 66 through 452) selection = (chain 'D' and resid 66 through 452) selection = (chain 'E' and resid 66 through 452) selection = (chain 'F' and resid 66 through 452) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.110 Find NCS groups from input model: 0.510 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2454 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 0.218 19540 Z= 0.398 Angle : 0.961 17.963 26636 Z= 0.493 Chirality : 0.048 0.242 3185 Planarity : 0.005 0.072 3264 Dihedral : 20.356 177.331 7629 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.74 % Favored : 94.75 % Rotamer: Outliers : 0.30 % Allowed : 17.07 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2364 helix: -1.03 (0.16), residues: 721 sheet: 0.19 (0.21), residues: 599 loop : -0.98 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 161 TYR 0.024 0.002 TYR C 147 PHE 0.025 0.002 PHE B 244 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.40 (19540) covalent geometry : angle 0.96104 / 0.49 (26636) hydrogen bonds : bond 0.15680 / 11.19 ( 758) hydrogen bonds : angle 7.39318 / 5.15 ( 2173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 358 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLU cc_start: 0.5649 (tt0) cc_final: 0.5431 (tt0) REVERT: F 96 ASP cc_start: 0.4655 (m-30) cc_final: 0.4432 (m-30) REVERT: F 225 MET cc_start: 0.5346 (pmm) cc_final: 0.5130 (pmm) REVERT: F 315 MET cc_start: 0.3607 (mtm) cc_final: 0.3088 (mmm) outliers start: 6 outliers final: 3 residues processed: 363 average time/residue: 0.1396 time to fit residues: 78.1099 Evaluate side-chains 245 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 242 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 350 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.083501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.060905 restraints weight = 48143.001| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.99 r_work: 0.2757 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 19540 Z= 0.312 Angle : 0.773 10.253 26636 Z= 0.402 Chirality : 0.048 0.237 3185 Planarity : 0.005 0.049 3264 Dihedral : 19.591 178.121 3227 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.30 % Favored : 96.53 % Rotamer: Outliers : 4.18 % Allowed : 18.27 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2364 helix: 0.67 (0.19), residues: 733 sheet: 0.12 (0.21), residues: 623 loop : -0.55 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 408 TYR 0.018 0.002 TYR A 120 PHE 0.019 0.002 PHE A 166 HIS 0.007 0.002 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.31 (19540) covalent geometry : angle 0.77345 / 0.40 (26636) hydrogen bonds : bond 0.05146 / 3.51 ( 758) hydrogen bonds : angle 5.70291 / 3.95 ( 2173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 248 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 MET cc_start: 0.8057 (tpt) cc_final: 0.7724 (tpt) REVERT: D 232 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.8897 (p) REVERT: D 279 VAL cc_start: 0.8985 (t) cc_final: 0.8763 (p) REVERT: C 143 GLU cc_start: 0.7924 (tp30) cc_final: 0.7167 (tm-30) REVERT: C 298 GLU cc_start: 0.8880 (tt0) cc_final: 0.8664 (tm-30) REVERT: C 403 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8567 (p0) REVERT: B 398 GLU cc_start: 0.8767 (pt0) cc_final: 0.8425 (pm20) REVERT: F 176 MET cc_start: 0.9363 (ptt) cc_final: 0.8774 (ppp) REVERT: F 177 SER cc_start: 0.7583 (OUTLIER) cc_final: 0.7208 (t) REVERT: F 192 GLU cc_start: 0.9213 (mp0) cc_final: 0.8861 (tm-30) REVERT: F 297 MET cc_start: 0.9094 (mmt) cc_final: 0.8721 (mmt) REVERT: E 225 MET cc_start: 0.8439 (tpp) cc_final: 0.7929 (tpp) REVERT: E 231 ASP cc_start: 0.8449 (t0) cc_final: 0.8199 (t0) REVERT: E 272 GLU cc_start: 0.9134 (pt0) cc_final: 0.8538 (mt-10) outliers start: 84 outliers final: 43 residues processed: 315 average time/residue: 0.1186 time to fit residues: 61.0445 Evaluate side-chains 272 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 236 PHE Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 441 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 93 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 153 GLN C 403 ASN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.063238 restraints weight = 47324.309| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.01 r_work: 0.2814 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19540 Z= 0.132 Angle : 0.642 11.177 26636 Z= 0.335 Chirality : 0.045 0.208 3185 Planarity : 0.004 0.043 3264 Dihedral : 19.003 177.959 3224 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.60 % Favored : 96.24 % Rotamer: Outliers : 2.44 % Allowed : 19.26 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2364 helix: 1.29 (0.19), residues: 732 sheet: 0.29 (0.21), residues: 613 loop : -0.23 (0.21), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 224 TYR 0.016 0.001 TYR A 120 PHE 0.010 0.001 PHE F 144 HIS 0.010 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (19540) covalent geometry : angle 0.64170 / 0.34 (26636) hydrogen bonds : bond 0.04166 / 2.85 ( 758) hydrogen bonds : angle 5.20006 / 3.59 ( 2173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8937 (mtp) cc_final: 0.8590 (mtp) REVERT: D 279 VAL cc_start: 0.8979 (t) cc_final: 0.8753 (p) REVERT: C 143 GLU cc_start: 0.7938 (tp30) cc_final: 0.7085 (tm-30) REVERT: C 152 MET cc_start: 0.9309 (mmm) cc_final: 0.8887 (tpp) REVERT: C 153 GLN cc_start: 0.9121 (mm110) cc_final: 0.8826 (mm-40) REVERT: C 298 GLU cc_start: 0.8911 (tt0) cc_final: 0.8543 (tm-30) REVERT: B 124 GLU cc_start: 0.8125 (tp30) cc_final: 0.7899 (tp30) REVERT: B 198 MET cc_start: 0.9123 (ttp) cc_final: 0.8909 (tpp) REVERT: B 304 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9189 (tt) REVERT: B 398 GLU cc_start: 0.8828 (pt0) cc_final: 0.8498 (pm20) REVERT: B 432 LEU cc_start: 0.9033 (mp) cc_final: 0.8804 (tt) REVERT: A 124 GLU cc_start: 0.8411 (tt0) cc_final: 0.7964 (pt0) REVERT: A 219 THR cc_start: 0.8063 (m) cc_final: 0.7795 (p) REVERT: A 367 ASP cc_start: 0.9247 (m-30) cc_final: 0.8973 (m-30) REVERT: F 176 MET cc_start: 0.9287 (ptt) cc_final: 0.8727 (ppp) REVERT: F 177 SER cc_start: 0.7385 (OUTLIER) cc_final: 0.6752 (t) REVERT: F 192 GLU cc_start: 0.9200 (mp0) cc_final: 0.8946 (tm-30) REVERT: F 217 GLU cc_start: 0.9041 (tp30) cc_final: 0.8694 (pp20) REVERT: F 297 MET cc_start: 0.9096 (mmt) cc_final: 0.8635 (mmt) REVERT: F 327 ASP cc_start: 0.9133 (t0) cc_final: 0.8876 (t0) REVERT: E 231 ASP cc_start: 0.8357 (t0) cc_final: 0.8156 (t0) REVERT: E 236 PHE cc_start: 0.9473 (OUTLIER) cc_final: 0.8508 (t80) REVERT: E 272 GLU cc_start: 0.9091 (pt0) cc_final: 0.8573 (mt-10) outliers start: 49 outliers final: 29 residues processed: 298 average time/residue: 0.1208 time to fit residues: 58.3519 Evaluate side-chains 257 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 199 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.061113 restraints weight = 47790.379| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 4.03 r_work: 0.2767 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19540 Z= 0.228 Angle : 0.647 12.651 26636 Z= 0.335 Chirality : 0.045 0.215 3185 Planarity : 0.004 0.045 3264 Dihedral : 18.558 178.572 3224 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer: Outliers : 3.53 % Allowed : 20.01 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2364 helix: 1.34 (0.20), residues: 734 sheet: 0.27 (0.21), residues: 620 loop : -0.20 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 224 TYR 0.018 0.001 TYR A 120 PHE 0.013 0.001 PHE B 144 HIS 0.007 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.23 (19540) covalent geometry : angle 0.64716 / 0.34 (26636) hydrogen bonds : bond 0.04235 / 2.92 ( 758) hydrogen bonds : angle 5.07842 / 3.50 ( 2173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 224 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9478 (OUTLIER) cc_final: 0.8983 (p) REVERT: D 242 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.7150 (m-70) REVERT: C 143 GLU cc_start: 0.7994 (tp30) cc_final: 0.7191 (tm-30) REVERT: C 152 MET cc_start: 0.9321 (mmm) cc_final: 0.8895 (tpp) REVERT: C 153 GLN cc_start: 0.9182 (mm110) cc_final: 0.8881 (mm-40) REVERT: C 298 GLU cc_start: 0.9009 (tt0) cc_final: 0.8733 (tm-30) REVERT: B 398 GLU cc_start: 0.8904 (pt0) cc_final: 0.8614 (pm20) REVERT: B 432 LEU cc_start: 0.9066 (mp) cc_final: 0.8839 (tt) REVERT: A 129 GLN cc_start: 0.8849 (tp40) cc_final: 0.8541 (tp-100) REVERT: A 219 THR cc_start: 0.8080 (m) cc_final: 0.7823 (p) REVERT: A 367 ASP cc_start: 0.9240 (m-30) cc_final: 0.8946 (m-30) REVERT: F 165 ASP cc_start: 0.8953 (m-30) cc_final: 0.8631 (t0) REVERT: F 176 MET cc_start: 0.9284 (ptt) cc_final: 0.8733 (ppp) REVERT: F 192 GLU cc_start: 0.9187 (mp0) cc_final: 0.8934 (tm-30) REVERT: F 327 ASP cc_start: 0.9179 (t0) cc_final: 0.8938 (t0) REVERT: E 227 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8289 (mp0) REVERT: E 231 ASP cc_start: 0.8456 (t0) cc_final: 0.8247 (t0) REVERT: E 398 GLU cc_start: 0.8411 (pt0) cc_final: 0.8178 (pm20) outliers start: 71 outliers final: 46 residues processed: 279 average time/residue: 0.1084 time to fit residues: 50.0036 Evaluate side-chains 254 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 350 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 99 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 73 optimal weight: 0.0070 chunk 235 optimal weight: 30.0000 chunk 210 optimal weight: 6.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.086121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.063794 restraints weight = 46992.504| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.01 r_work: 0.2830 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19540 Z= 0.112 Angle : 0.608 11.248 26636 Z= 0.313 Chirality : 0.044 0.284 3185 Planarity : 0.004 0.057 3264 Dihedral : 18.095 179.199 3224 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.40 % Rotamer: Outliers : 2.69 % Allowed : 20.51 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2364 helix: 1.43 (0.20), residues: 740 sheet: 0.33 (0.21), residues: 616 loop : -0.15 (0.22), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 248 TYR 0.016 0.001 TYR A 120 PHE 0.010 0.001 PHE D 316 HIS 0.007 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (19540) covalent geometry : angle 0.60824 / 0.31 (26636) hydrogen bonds : bond 0.03558 / 2.45 ( 758) hydrogen bonds : angle 4.80672 / 3.31 ( 2173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 0.737 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: D 196 GLU cc_start: 0.9488 (OUTLIER) cc_final: 0.9176 (tp30) REVERT: D 242 HIS cc_start: 0.7458 (t-90) cc_final: 0.7254 (t-90) REVERT: D 348 ASN cc_start: 0.8988 (t0) cc_final: 0.8768 (t0) REVERT: C 139 ASP cc_start: 0.3531 (t0) cc_final: 0.3133 (t0) REVERT: C 143 GLU cc_start: 0.7918 (tp30) cc_final: 0.7148 (tm-30) REVERT: C 152 MET cc_start: 0.9339 (mmm) cc_final: 0.8992 (tpt) REVERT: C 153 GLN cc_start: 0.9176 (mm110) cc_final: 0.8894 (mm-40) REVERT: C 198 MET cc_start: 0.9416 (ttp) cc_final: 0.9173 (ttp) REVERT: C 298 GLU cc_start: 0.8992 (tt0) cc_final: 0.8720 (tm-30) REVERT: C 327 ASP cc_start: 0.8311 (t0) cc_final: 0.8105 (t0) REVERT: B 398 GLU cc_start: 0.8896 (pt0) cc_final: 0.8651 (pm20) REVERT: B 432 LEU cc_start: 0.9078 (mp) cc_final: 0.8825 (tt) REVERT: A 124 GLU cc_start: 0.8457 (tt0) cc_final: 0.7986 (pt0) REVERT: A 129 GLN cc_start: 0.8856 (tp40) cc_final: 0.8536 (tp-100) REVERT: A 219 THR cc_start: 0.8092 (m) cc_final: 0.7865 (p) REVERT: A 350 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8473 (m-30) REVERT: A 367 ASP cc_start: 0.9208 (m-30) cc_final: 0.8875 (m-30) REVERT: F 96 ASP cc_start: 0.9088 (m-30) cc_final: 0.8831 (p0) REVERT: F 165 ASP cc_start: 0.9005 (m-30) cc_final: 0.8681 (t0) REVERT: F 174 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.9077 (p) REVERT: F 176 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8638 (ppp) REVERT: F 192 GLU cc_start: 0.9178 (mp0) cc_final: 0.8963 (tm-30) REVERT: F 242 HIS cc_start: 0.8016 (m90) cc_final: 0.7230 (m170) REVERT: F 297 MET cc_start: 0.9073 (mmt) cc_final: 0.8592 (mmt) REVERT: E 236 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8440 (t80) REVERT: E 272 GLU cc_start: 0.9099 (pt0) cc_final: 0.8703 (mt-10) outliers start: 54 outliers final: 27 residues processed: 303 average time/residue: 0.1209 time to fit residues: 59.9658 Evaluate side-chains 271 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 65 optimal weight: 0.8980 chunk 181 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 242 HIS B 403 ASN A 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.061005 restraints weight = 47866.485| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.03 r_work: 0.2771 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19540 Z= 0.228 Angle : 0.648 9.980 26636 Z= 0.332 Chirality : 0.045 0.242 3185 Planarity : 0.004 0.038 3264 Dihedral : 18.061 179.533 3224 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 2.79 % Allowed : 21.35 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2364 helix: 1.47 (0.20), residues: 740 sheet: 0.28 (0.21), residues: 618 loop : -0.22 (0.22), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 224 TYR 0.018 0.002 TYR B 147 PHE 0.018 0.001 PHE C 263 HIS 0.006 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (19540) covalent geometry : angle 0.64773 / 0.33 (26636) hydrogen bonds : bond 0.03930 / 2.70 ( 758) hydrogen bonds : angle 4.84749 / 3.34 ( 2173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9012 (p) REVERT: D 348 ASN cc_start: 0.9024 (t0) cc_final: 0.8801 (t0) REVERT: C 143 GLU cc_start: 0.8034 (tp30) cc_final: 0.7422 (tm-30) REVERT: C 152 MET cc_start: 0.9314 (mmm) cc_final: 0.8959 (tpt) REVERT: C 153 GLN cc_start: 0.9220 (mm110) cc_final: 0.8910 (mm-40) REVERT: C 198 MET cc_start: 0.9468 (ttp) cc_final: 0.9199 (ttp) REVERT: C 242 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7382 (m90) REVERT: C 298 GLU cc_start: 0.9005 (tt0) cc_final: 0.8766 (tm-30) REVERT: B 147 TYR cc_start: 0.8356 (t80) cc_final: 0.8054 (t80) REVERT: B 398 GLU cc_start: 0.8944 (pt0) cc_final: 0.8666 (pm20) REVERT: B 432 LEU cc_start: 0.9115 (mp) cc_final: 0.8825 (tt) REVERT: A 124 GLU cc_start: 0.8554 (tt0) cc_final: 0.8070 (pt0) REVERT: A 129 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8583 (tp-100) REVERT: A 198 MET cc_start: 0.9175 (ttm) cc_final: 0.8749 (mtp) REVERT: A 219 THR cc_start: 0.8108 (m) cc_final: 0.7869 (p) REVERT: A 367 ASP cc_start: 0.9253 (m-30) cc_final: 0.8958 (m-30) REVERT: F 96 ASP cc_start: 0.9101 (m-30) cc_final: 0.8833 (p0) REVERT: F 165 ASP cc_start: 0.9020 (m-30) cc_final: 0.8694 (t0) REVERT: F 176 MET cc_start: 0.9214 (ptt) cc_final: 0.8820 (ppp) REVERT: F 189 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6123 (tp-100) REVERT: F 192 GLU cc_start: 0.9194 (mp0) cc_final: 0.8922 (tm-30) REVERT: F 297 MET cc_start: 0.9072 (mmt) cc_final: 0.8584 (mmt) REVERT: E 152 MET cc_start: 0.9125 (tpt) cc_final: 0.8882 (tpt) REVERT: E 236 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.8371 (t80) REVERT: E 272 GLU cc_start: 0.9123 (pt0) cc_final: 0.8593 (mt-10) outliers start: 56 outliers final: 38 residues processed: 268 average time/residue: 0.1196 time to fit residues: 52.9181 Evaluate side-chains 259 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 139 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 235 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.060939 restraints weight = 47892.725| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.04 r_work: 0.2773 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19540 Z= 0.202 Angle : 0.643 11.168 26636 Z= 0.329 Chirality : 0.044 0.222 3185 Planarity : 0.004 0.038 3264 Dihedral : 17.999 178.754 3224 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.90 % Rotamer: Outliers : 3.38 % Allowed : 20.91 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2364 helix: 1.50 (0.20), residues: 740 sheet: 0.22 (0.21), residues: 623 loop : -0.26 (0.22), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 224 TYR 0.022 0.001 TYR E 147 PHE 0.015 0.001 PHE C 263 HIS 0.018 0.002 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (19540) covalent geometry : angle 0.64298 / 0.33 (26636) hydrogen bonds : bond 0.03809 / 2.63 ( 758) hydrogen bonds : angle 4.78473 / 3.29 ( 2173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 223 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 GLU cc_start: 0.9533 (OUTLIER) cc_final: 0.9227 (tp30) REVERT: D 232 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9012 (p) REVERT: D 348 ASN cc_start: 0.9062 (t0) cc_final: 0.8728 (t0) REVERT: C 143 GLU cc_start: 0.8087 (tp30) cc_final: 0.7516 (tm-30) REVERT: C 152 MET cc_start: 0.9330 (mmm) cc_final: 0.8979 (tpt) REVERT: C 153 GLN cc_start: 0.9225 (mm110) cc_final: 0.8910 (mm-40) REVERT: C 198 MET cc_start: 0.9466 (ttp) cc_final: 0.9175 (ttp) REVERT: C 298 GLU cc_start: 0.9013 (tt0) cc_final: 0.8780 (tm-30) REVERT: C 327 ASP cc_start: 0.8421 (t0) cc_final: 0.8200 (t0) REVERT: B 147 TYR cc_start: 0.8367 (t80) cc_final: 0.8104 (t80) REVERT: B 398 GLU cc_start: 0.8948 (pt0) cc_final: 0.8703 (pm20) REVERT: B 432 LEU cc_start: 0.9104 (mp) cc_final: 0.8812 (tt) REVERT: A 198 MET cc_start: 0.9171 (ttm) cc_final: 0.8713 (mtp) REVERT: A 219 THR cc_start: 0.8094 (m) cc_final: 0.7851 (p) REVERT: A 350 ASP cc_start: 0.8671 (m-30) cc_final: 0.8390 (m-30) REVERT: A 367 ASP cc_start: 0.9255 (m-30) cc_final: 0.8956 (m-30) REVERT: F 96 ASP cc_start: 0.9089 (m-30) cc_final: 0.8847 (p0) REVERT: F 165 ASP cc_start: 0.9047 (m-30) cc_final: 0.8703 (t0) REVERT: F 176 MET cc_start: 0.9213 (ptt) cc_final: 0.8786 (ppp) REVERT: F 189 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6133 (tp-100) REVERT: F 192 GLU cc_start: 0.9183 (mp0) cc_final: 0.8929 (tm-30) REVERT: F 297 MET cc_start: 0.9039 (mmt) cc_final: 0.8576 (mmt) REVERT: E 231 ASP cc_start: 0.8477 (t0) cc_final: 0.8217 (t0) REVERT: E 236 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8280 (t80) REVERT: E 272 GLU cc_start: 0.9105 (pt0) cc_final: 0.8593 (mt-10) outliers start: 68 outliers final: 47 residues processed: 276 average time/residue: 0.1264 time to fit residues: 57.4476 Evaluate side-chains 269 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain E residue 390 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 98 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.061415 restraints weight = 47643.606| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.04 r_work: 0.2781 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19540 Z= 0.165 Angle : 0.625 11.873 26636 Z= 0.321 Chirality : 0.044 0.227 3185 Planarity : 0.004 0.044 3264 Dihedral : 17.885 178.213 3224 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.98 % Rotamer: Outliers : 2.74 % Allowed : 21.70 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2364 helix: 1.54 (0.20), residues: 739 sheet: 0.19 (0.21), residues: 623 loop : -0.25 (0.22), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 161 TYR 0.018 0.001 TYR E 147 PHE 0.018 0.001 PHE C 280 HIS 0.005 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (19540) covalent geometry : angle 0.62504 / 0.32 (26636) hydrogen bonds : bond 0.03660 / 2.52 ( 758) hydrogen bonds : angle 4.70110 / 3.23 ( 2173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 GLU cc_start: 0.9512 (OUTLIER) cc_final: 0.9205 (tp30) REVERT: D 232 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9006 (p) REVERT: D 348 ASN cc_start: 0.9063 (t0) cc_final: 0.8761 (t0) REVERT: C 143 GLU cc_start: 0.8074 (tp30) cc_final: 0.7621 (tm-30) REVERT: C 152 MET cc_start: 0.9299 (mmm) cc_final: 0.8957 (tpt) REVERT: C 153 GLN cc_start: 0.9205 (mm110) cc_final: 0.8914 (mm-40) REVERT: C 198 MET cc_start: 0.9450 (ttp) cc_final: 0.9186 (ttp) REVERT: C 298 GLU cc_start: 0.8990 (tt0) cc_final: 0.8777 (tm-30) REVERT: C 327 ASP cc_start: 0.8412 (t0) cc_final: 0.8174 (t0) REVERT: B 156 ARG cc_start: 0.9328 (ttm-80) cc_final: 0.9052 (ttm170) REVERT: B 432 LEU cc_start: 0.9099 (mp) cc_final: 0.8792 (tt) REVERT: A 124 GLU cc_start: 0.8743 (tt0) cc_final: 0.8156 (pt0) REVERT: A 198 MET cc_start: 0.9152 (ttm) cc_final: 0.8695 (mtp) REVERT: A 219 THR cc_start: 0.8119 (m) cc_final: 0.7874 (p) REVERT: A 225 MET cc_start: 0.8836 (ppp) cc_final: 0.8548 (ppp) REVERT: A 350 ASP cc_start: 0.8679 (m-30) cc_final: 0.8393 (m-30) REVERT: A 367 ASP cc_start: 0.9200 (m-30) cc_final: 0.8904 (m-30) REVERT: F 96 ASP cc_start: 0.9092 (m-30) cc_final: 0.8872 (p0) REVERT: F 165 ASP cc_start: 0.9053 (m-30) cc_final: 0.8684 (t0) REVERT: F 176 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8785 (ppp) REVERT: F 189 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6135 (tp-100) REVERT: F 192 GLU cc_start: 0.9176 (mp0) cc_final: 0.8933 (tm-30) REVERT: F 297 MET cc_start: 0.9014 (mmt) cc_final: 0.8568 (mmt) REVERT: E 165 ASP cc_start: 0.8523 (m-30) cc_final: 0.7689 (t0) REVERT: E 231 ASP cc_start: 0.8475 (t0) cc_final: 0.8211 (t0) REVERT: E 236 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8289 (t80) REVERT: E 272 GLU cc_start: 0.9097 (pt0) cc_final: 0.8624 (mt-10) REVERT: E 297 MET cc_start: 0.9269 (tpp) cc_final: 0.8699 (mmm) outliers start: 55 outliers final: 43 residues processed: 274 average time/residue: 0.1203 time to fit residues: 54.5617 Evaluate side-chains 266 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain E residue 390 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 93 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 207 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.061243 restraints weight = 47983.055| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.03 r_work: 0.2784 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19540 Z= 0.164 Angle : 0.635 12.418 26636 Z= 0.324 Chirality : 0.044 0.203 3185 Planarity : 0.004 0.042 3264 Dihedral : 17.762 177.025 3224 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 2.74 % Allowed : 21.80 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2364 helix: 1.57 (0.20), residues: 739 sheet: 0.19 (0.21), residues: 621 loop : -0.32 (0.22), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 284 TYR 0.019 0.001 TYR B 147 PHE 0.017 0.001 PHE C 263 HIS 0.008 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (19540) covalent geometry : angle 0.63512 / 0.32 (26636) hydrogen bonds : bond 0.03618 / 2.48 ( 758) hydrogen bonds : angle 4.68433 / 3.22 ( 2173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 GLU cc_start: 0.9506 (OUTLIER) cc_final: 0.9200 (tp30) REVERT: D 232 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.8995 (p) REVERT: D 348 ASN cc_start: 0.9087 (t0) cc_final: 0.8803 (t0) REVERT: D 434 LYS cc_start: 0.8993 (tptp) cc_final: 0.8704 (tppt) REVERT: C 143 GLU cc_start: 0.8107 (tp30) cc_final: 0.7645 (tm-30) REVERT: C 152 MET cc_start: 0.9320 (mmm) cc_final: 0.8960 (tpt) REVERT: C 153 GLN cc_start: 0.9204 (mm110) cc_final: 0.8897 (mm-40) REVERT: C 198 MET cc_start: 0.9435 (ttp) cc_final: 0.9189 (ttp) REVERT: C 298 GLU cc_start: 0.9001 (tt0) cc_final: 0.8796 (tm-30) REVERT: C 327 ASP cc_start: 0.8414 (t0) cc_final: 0.8170 (t0) REVERT: B 147 TYR cc_start: 0.8309 (t80) cc_final: 0.8067 (t80) REVERT: B 432 LEU cc_start: 0.9100 (mp) cc_final: 0.8779 (tt) REVERT: A 124 GLU cc_start: 0.8750 (tt0) cc_final: 0.8204 (pt0) REVERT: A 198 MET cc_start: 0.9159 (ttm) cc_final: 0.8685 (mtp) REVERT: A 219 THR cc_start: 0.8141 (m) cc_final: 0.7896 (p) REVERT: A 225 MET cc_start: 0.8843 (ppp) cc_final: 0.8523 (ppp) REVERT: A 350 ASP cc_start: 0.8678 (m-30) cc_final: 0.8392 (m-30) REVERT: A 367 ASP cc_start: 0.9199 (m-30) cc_final: 0.8898 (m-30) REVERT: F 96 ASP cc_start: 0.9088 (m-30) cc_final: 0.8882 (p0) REVERT: F 165 ASP cc_start: 0.9078 (m-30) cc_final: 0.8669 (t0) REVERT: F 176 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8778 (ppp) REVERT: F 189 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6139 (tp-100) REVERT: F 192 GLU cc_start: 0.9185 (mp0) cc_final: 0.8944 (tm-30) REVERT: F 297 MET cc_start: 0.8991 (mmt) cc_final: 0.8568 (mmt) REVERT: E 152 MET cc_start: 0.9138 (tpt) cc_final: 0.8874 (tpt) REVERT: E 165 ASP cc_start: 0.8545 (m-30) cc_final: 0.7696 (t0) REVERT: E 231 ASP cc_start: 0.8492 (t0) cc_final: 0.8211 (t0) REVERT: E 236 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.8400 (t80) REVERT: E 272 GLU cc_start: 0.9122 (pt0) cc_final: 0.8637 (mt-10) REVERT: E 297 MET cc_start: 0.9260 (tpp) cc_final: 0.8823 (mmm) outliers start: 55 outliers final: 46 residues processed: 271 average time/residue: 0.1276 time to fit residues: 56.6599 Evaluate side-chains 267 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain E residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 118 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.061466 restraints weight = 47803.587| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.04 r_work: 0.2783 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19540 Z= 0.169 Angle : 0.652 12.820 26636 Z= 0.333 Chirality : 0.044 0.287 3185 Planarity : 0.004 0.043 3264 Dihedral : 17.668 176.577 3224 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 2.64 % Allowed : 22.00 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2364 helix: 1.55 (0.20), residues: 739 sheet: 0.21 (0.21), residues: 621 loop : -0.36 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 284 TYR 0.017 0.001 TYR E 147 PHE 0.017 0.001 PHE C 263 HIS 0.009 0.001 HIS D 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (19540) covalent geometry : angle 0.65232 / 0.33 (26636) hydrogen bonds : bond 0.03633 / 2.49 ( 758) hydrogen bonds : angle 4.70504 / 3.25 ( 2173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 GLU cc_start: 0.9516 (OUTLIER) cc_final: 0.9222 (tp30) REVERT: D 232 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9001 (p) REVERT: D 348 ASN cc_start: 0.9083 (t0) cc_final: 0.8815 (t0) REVERT: C 143 GLU cc_start: 0.8098 (tp30) cc_final: 0.7674 (tm-30) REVERT: C 152 MET cc_start: 0.9364 (mmm) cc_final: 0.8994 (tpt) REVERT: C 153 GLN cc_start: 0.9203 (mm110) cc_final: 0.8894 (mm-40) REVERT: C 198 MET cc_start: 0.9455 (ttp) cc_final: 0.9218 (ttp) REVERT: C 298 GLU cc_start: 0.8985 (tt0) cc_final: 0.8778 (tm-30) REVERT: C 327 ASP cc_start: 0.8409 (t0) cc_final: 0.8165 (t0) REVERT: B 147 TYR cc_start: 0.8314 (t80) cc_final: 0.8110 (t80) REVERT: B 432 LEU cc_start: 0.9101 (mp) cc_final: 0.8771 (tt) REVERT: A 124 GLU cc_start: 0.8771 (tt0) cc_final: 0.8226 (pt0) REVERT: A 198 MET cc_start: 0.9072 (ttm) cc_final: 0.8611 (mtp) REVERT: A 219 THR cc_start: 0.8164 (m) cc_final: 0.7917 (p) REVERT: A 225 MET cc_start: 0.8814 (ppp) cc_final: 0.8538 (ppp) REVERT: A 297 MET cc_start: 0.8281 (mmm) cc_final: 0.7969 (mmm) REVERT: A 350 ASP cc_start: 0.8704 (m-30) cc_final: 0.8427 (m-30) REVERT: A 367 ASP cc_start: 0.9183 (m-30) cc_final: 0.8869 (m-30) REVERT: F 96 ASP cc_start: 0.9091 (m-30) cc_final: 0.8884 (p0) REVERT: F 165 ASP cc_start: 0.9104 (m-30) cc_final: 0.8699 (t0) REVERT: F 176 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8798 (ppp) REVERT: F 189 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6148 (tp-100) REVERT: F 192 GLU cc_start: 0.9182 (mp0) cc_final: 0.8951 (tm-30) REVERT: F 242 HIS cc_start: 0.7788 (m90) cc_final: 0.7063 (m170) REVERT: E 152 MET cc_start: 0.9133 (tpt) cc_final: 0.8857 (tpt) REVERT: E 165 ASP cc_start: 0.8531 (m-30) cc_final: 0.7694 (t0) REVERT: E 227 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: E 231 ASP cc_start: 0.8507 (t0) cc_final: 0.8216 (t0) REVERT: E 236 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8374 (t80) REVERT: E 272 GLU cc_start: 0.9113 (pt0) cc_final: 0.8661 (mt-10) REVERT: E 297 MET cc_start: 0.9260 (tpp) cc_final: 0.8650 (mmm) outliers start: 53 outliers final: 46 residues processed: 265 average time/residue: 0.1248 time to fit residues: 54.7567 Evaluate side-chains 259 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain E residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 9 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 0.0060 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.060437 restraints weight = 48234.994| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.04 r_work: 0.2765 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19540 Z= 0.198 Angle : 0.672 12.922 26636 Z= 0.341 Chirality : 0.044 0.191 3185 Planarity : 0.004 0.043 3264 Dihedral : 17.622 176.508 3224 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 2.79 % Allowed : 21.85 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 2364 helix: 1.55 (0.20), residues: 737 sheet: 0.24 (0.22), residues: 616 loop : -0.36 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 284 TYR 0.022 0.002 TYR D 145 PHE 0.018 0.001 PHE C 263 HIS 0.005 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (19540) covalent geometry : angle 0.67221 / 0.34 (26636) hydrogen bonds : bond 0.03731 / 2.55 ( 758) hydrogen bonds : angle 4.74085 / 3.27 ( 2173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4282.35 seconds wall clock time: 74 minutes 18.74 seconds (4458.74 seconds total)