Starting phenix.real_space_refine on Sat Aug 23 17:37:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2j_42916/08_2025/8v2j_42916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2j_42916/08_2025/8v2j_42916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v2j_42916/08_2025/8v2j_42916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2j_42916/08_2025/8v2j_42916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v2j_42916/08_2025/8v2j_42916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2j_42916/08_2025/8v2j_42916.map" } resolution = 2.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 8537 2.51 5 N 2305 2.21 5 O 2634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13580 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3332 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 3334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3334 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3398 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3394 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.62, per 1000 atoms: 0.27 Number of scatterers: 13580 At special positions: 0 Unit cell: (74.7, 78.435, 191.73, 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 92 16.00 P 10 15.00 Mg 2 11.99 O 2634 8.00 N 2305 7.00 C 8537 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: 1.25 Conformation dependent library (CDL) restraints added in 653.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 55.2% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.128A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.709A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.640A pdb=" N SER B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.319A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.620A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.061A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.906A pdb=" N TYR B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.709A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.564A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 392 removed outlier: 4.085A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.971A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.907A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 40 through 46 removed outlier: 4.134A pdb=" N LEU E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 108 through 127 removed outlier: 4.812A pdb=" N ASP E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 159 removed outlier: 3.625A pdb=" N SER E 145 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 196 removed outlier: 4.666A pdb=" N GLU E 194 " --> pdb=" O HIS E 190 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN E 195 " --> pdb=" O GLN E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 214 Processing helix chain 'E' and resid 221 through 237 removed outlier: 3.703A pdb=" N LEU E 225 " --> pdb=" O THR E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.833A pdb=" N ARG E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.166A pdb=" N TYR E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 324 through 337 Processing helix chain 'E' and resid 338 through 341 Processing helix chain 'E' and resid 373 through 391 removed outlier: 3.935A pdb=" N LEU E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 401 removed outlier: 3.995A pdb=" N TYR E 398 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 401 " --> pdb=" O TRP E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 428 removed outlier: 3.877A pdb=" N PHE E 408 " --> pdb=" O ASP E 404 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 426 " --> pdb=" O TYR E 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 44 through 51 removed outlier: 4.042A pdb=" N SER A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 108 through 129 removed outlier: 3.884A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.659A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.649A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.104A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.608A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.909A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.065A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 3.891A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 44 through 51 removed outlier: 3.775A pdb=" N SER D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 82 through 85 removed outlier: 4.429A pdb=" N GLN D 85 " --> pdb=" O THR D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 82 through 85' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 110 through 128 removed outlier: 4.197A pdb=" N ILE D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 128 " --> pdb=" O LYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 4.607A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.597A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 277 through 282 removed outlier: 4.174A pdb=" N TYR D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.747A pdb=" N PHE D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 297 " --> pdb=" O ASN D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 338 removed outlier: 3.619A pdb=" N VAL D 328 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 401 removed outlier: 3.837A pdb=" N ALA D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 3.954A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 411 " --> pdb=" O TRP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 436 removed outlier: 3.730A pdb=" N PHE D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.315A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'E' and resid 90 through 92 removed outlier: 8.162A pdb=" N VAL E 91 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU E 65 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ILE E 64 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS E 6 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL E 66 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN E 8 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU E 3 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY E 132 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL E 5 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER E 138 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASN E 165 " --> pdb=" O GLN E 131 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHE E 133 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE E 167 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU E 135 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL E 169 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N HIS E 137 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR E 199 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N CYS E 201 " --> pdb=" O PRO E 268 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N PHE E 270 " --> pdb=" O CYS E 201 " (cutoff:3.500A) removed outlier: 13.187A pdb=" N ASP E 203 " --> pdb=" O PHE E 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.851A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N SER A 165 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.769A pdb=" N ILE D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE D 67 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N VAL D 66 " --> pdb=" O CYS D 4 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER D 6 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL D 68 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N HIS D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU D 3 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU D 136 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE D 5 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE D 138 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE D 7 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N SER D 140 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N VAL D 9 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN D 133 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE D 135 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE D 171 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS D 139 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS D 166 " --> pdb=" O CYS D 200 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE D 202 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU D 168 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL D 204 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER D 170 " --> pdb=" O VAL D 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'D' and resid 272 through 273 678 hydrogen bonds defined for protein. 2007 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4412 1.34 - 1.46: 3143 1.46 - 1.58: 6174 1.58 - 1.71: 17 1.71 - 1.83: 144 Bond restraints: 13890 Sorted by residual: bond pdb=" N TYR E 310 " pdb=" CA TYR E 310 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N VAL E 313 " pdb=" CA VAL E 313 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.80e+00 bond pdb=" N SER E 322 " pdb=" CA SER E 322 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.27e-02 6.20e+03 9.11e+00 bond pdb=" N ASP A 46 " pdb=" CA ASP A 46 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.73e+00 bond pdb=" N MET E 323 " pdb=" CA MET E 323 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.42e+00 ... (remaining 13885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 18289 2.41 - 4.81: 490 4.81 - 7.22: 102 7.22 - 9.62: 6 9.62 - 12.03: 2 Bond angle restraints: 18889 Sorted by residual: angle pdb=" CA ILE D 219 " pdb=" C ILE D 219 " pdb=" O ILE D 219 " ideal model delta sigma weight residual 121.68 117.01 4.67 7.90e-01 1.60e+00 3.49e+01 angle pdb=" N LYS E 324 " pdb=" CA LYS E 324 " pdb=" C LYS E 324 " ideal model delta sigma weight residual 113.18 106.89 6.29 1.33e+00 5.65e-01 2.23e+01 angle pdb=" CB MET E 406 " pdb=" CG MET E 406 " pdb=" SD MET E 406 " ideal model delta sigma weight residual 112.70 124.73 -12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CA ARG D 221 " pdb=" C ARG D 221 " pdb=" N PRO D 222 " ideal model delta sigma weight residual 117.78 121.90 -4.12 1.06e+00 8.90e-01 1.51e+01 angle pdb=" CB MET A 203 " pdb=" CG MET A 203 " pdb=" SD MET A 203 " ideal model delta sigma weight residual 112.70 124.21 -11.51 3.00e+00 1.11e-01 1.47e+01 ... (remaining 18884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.51: 7895 31.51 - 63.01: 289 63.01 - 94.52: 32 94.52 - 126.02: 1 126.02 - 157.53: 6 Dihedral angle restraints: 8223 sinusoidal: 3233 harmonic: 4990 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -133.20 -157.53 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C5' GTP D 501 " pdb=" O5' GTP D 501 " pdb=" PA GTP D 501 " pdb=" O3A GTP D 501 " ideal model delta sinusoidal sigma weight residual 69.27 -133.45 -157.28 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O5' GTP D 501 " pdb=" O3A GTP D 501 " pdb=" PA GTP D 501 " pdb=" PB GTP D 501 " ideal model delta sinusoidal sigma weight residual 274.12 139.23 134.89 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 8220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1627 0.059 - 0.118: 373 0.118 - 0.177: 74 0.177 - 0.236: 3 0.236 - 0.295: 1 Chirality restraints: 2078 Sorted by residual: chirality pdb=" CA ILE D 219 " pdb=" N ILE D 219 " pdb=" C ILE D 219 " pdb=" CB ILE D 219 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LYS E 324 " pdb=" N LYS E 324 " pdb=" C LYS E 324 " pdb=" CB LYS E 324 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA VAL E 313 " pdb=" N VAL E 313 " pdb=" C VAL E 313 " pdb=" CB VAL E 313 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 2075 not shown) Planarity restraints: 2463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 273 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO A 274 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 218 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C ASP D 218 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP D 218 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE D 219 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 128 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" CG ASP B 128 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP B 128 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 128 " -0.016 2.00e-02 2.50e+03 ... (remaining 2460 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 85 2.56 - 3.14: 10839 3.14 - 3.73: 22247 3.73 - 4.31: 31147 4.31 - 4.90: 52203 Nonbonded interactions: 116521 Sorted by model distance: nonbonded pdb=" O1G GTP D 501 " pdb="MG MG D 502 " model vdw 1.970 2.170 nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 1.996 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 2.004 2.170 nonbonded pdb=" O2B GTP D 501 " pdb="MG MG D 502 " model vdw 2.024 2.170 nonbonded pdb=" OE2 GLU D 71 " pdb="MG MG D 502 " model vdw 2.030 2.170 ... (remaining 116516 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 1 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 502)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 1 through 335 or (resid 336 and (name N or name CA or name \ C or name O or name CB )) or resid 337 through 501)) selection = (chain 'E' and (resid 1 through 281 or (resid 282 through 283 and (name N or nam \ e CA or name C or name O or name CB )) or resid 284 through 501)) } 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: 9.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.560 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 0.006 0.068 13890 Z= 0.282 Angle : 0.953 12.025 18889 Z= 0.515 Chirality : 0.052 0.295 2078 Planarity : 0.006 0.075 2463 Dihedral : 16.662 157.528 5027 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.42 % Allowed : 14.67 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.06 (0.20), residues: 1720 helix: 0.93 (0.18), residues: 776 sheet: -0.81 (0.33), residues: 244 loop : -0.53 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 84 TYR 0.032 0.002 TYR D 24 PHE 0.026 0.002 PHE E 81 TRP 0.013 0.002 TRP E 397 HIS 0.010 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00580 (13890) covalent geometry : angle 0.95305 (18889) hydrogen bonds : bond 0.06520 ( 678) hydrogen bonds : angle 5.45602 ( 2007) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 391 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 22 GLU cc_start: 0.6762 (tt0) cc_final: 0.6448 (mp0) REVERT: B 60 VAL cc_start: 0.8124 (t) cc_final: 0.7816 (t) REVERT: B 73 MET cc_start: 0.6968 (mtp) cc_final: 0.6706 (mtp) REVERT: B 83 GLN cc_start: 0.8242 (tt0) cc_final: 0.7995 (tt0) REVERT: B 94 GLN cc_start: 0.7285 (mt0) cc_final: 0.6205 (tm-30) REVERT: B 135 LEU cc_start: 0.7870 (tp) cc_final: 0.7666 (tp) REVERT: B 157 GLU cc_start: 0.7474 (tp30) cc_final: 0.6930 (mt-10) REVERT: B 161 ASP cc_start: 0.7680 (t70) cc_final: 0.7039 (p0) REVERT: B 192 LEU cc_start: 0.7150 (mp) cc_final: 0.6913 (mt) REVERT: B 242 PHE cc_start: 0.7718 (m-80) cc_final: 0.7486 (m-80) REVERT: B 280 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7497 (mp10) REVERT: B 309 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6749 (mtt180) REVERT: B 318 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7451 (mtp180) REVERT: B 376 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6138 (mm-30) REVERT: B 383 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6757 (tm-30) REVERT: E 88 ASP cc_start: 0.6708 (t0) cc_final: 0.6108 (t0) REVERT: E 112 LEU cc_start: 0.7328 (mm) cc_final: 0.7111 (mt) REVERT: E 114 ASP cc_start: 0.7263 (m-30) cc_final: 0.7024 (m-30) REVERT: E 123 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5902 (mm-30) REVERT: E 134 GLN cc_start: 0.8084 (tt0) cc_final: 0.7689 (pt0) REVERT: E 161 ASP cc_start: 0.7912 (t70) cc_final: 0.7349 (p0) REVERT: E 241 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.7061 (mtm110) REVERT: E 291 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7058 (pp30) REVERT: E 298 ASN cc_start: 0.7321 (t0) cc_final: 0.6798 (t0) REVERT: E 344 TRP cc_start: 0.7940 (p-90) cc_final: 0.7670 (p-90) REVERT: E 362 LYS cc_start: 0.7553 (mmtm) cc_final: 0.6702 (ttpt) REVERT: E 383 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6787 (tm-30) REVERT: E 406 MET cc_start: 0.6374 (tpp) cc_final: 0.6063 (tpp) REVERT: A 24 TYR cc_start: 0.7326 (m-10) cc_final: 0.6633 (m-10) REVERT: A 172 TYR cc_start: 0.7257 (t80) cc_final: 0.5872 (t80) REVERT: A 279 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7243 (mp0) REVERT: A 280 LYS cc_start: 0.3971 (mmtt) cc_final: 0.3454 (tptp) REVERT: A 386 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6949 (mm-30) REVERT: D 1 MET cc_start: 0.1859 (tmm) cc_final: 0.1654 (tmm) REVERT: D 49 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.4917 (t80) REVERT: D 55 GLU cc_start: 0.7762 (tt0) cc_final: 0.6682 (mp0) REVERT: D 214 ARG cc_start: 0.7636 (ttm170) cc_final: 0.7368 (ttm110) REVERT: D 220 GLU cc_start: 0.7421 (tp30) cc_final: 0.7125 (pt0) REVERT: D 279 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7204 (mp0) REVERT: D 326 LYS cc_start: 0.7876 (tttt) cc_final: 0.6735 (mptt) REVERT: D 370 LYS cc_start: 0.6751 (tptt) cc_final: 0.6339 (tptp) REVERT: D 390 ARG cc_start: 0.6934 (mtm110) cc_final: 0.6523 (ttp80) REVERT: D 392 ASP cc_start: 0.7652 (m-30) cc_final: 0.7341 (m-30) outliers start: 6 outliers final: 1 residues processed: 393 average time/residue: 0.7013 time to fit residues: 298.4804 Evaluate side-chains 239 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain D residue 49 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 131 GLN B 165 ASN B 204 ASN B 247 ASN B 375 GLN B 396 HIS E 6 HIS E 131 GLN E 134 GLN A 128 GLN A 206 ASN A 293 ASN A 358 GLN D 101 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 206 ASN D 266 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.123553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111049 restraints weight = 19476.131| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.71 r_work: 0.3505 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13890 Z= 0.137 Angle : 0.560 8.541 18889 Z= 0.287 Chirality : 0.044 0.142 2078 Planarity : 0.004 0.040 2463 Dihedral : 10.730 157.337 1927 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.36 % Allowed : 15.57 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.62 (0.20), residues: 1720 helix: 1.45 (0.18), residues: 806 sheet: -0.48 (0.31), residues: 286 loop : -0.39 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 390 TYR 0.020 0.001 TYR D 24 PHE 0.015 0.002 PHE B 20 TRP 0.010 0.001 TRP A 21 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00305 (13890) covalent geometry : angle 0.56033 (18889) hydrogen bonds : bond 0.04394 ( 678) hydrogen bonds : angle 4.65728 ( 2007) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 257 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: B 3 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6242 (mm-30) REVERT: B 41 ASP cc_start: 0.7113 (t0) cc_final: 0.6890 (t0) REVERT: B 44 LEU cc_start: 0.8018 (mt) cc_final: 0.7816 (mp) REVERT: B 94 GLN cc_start: 0.7266 (mt0) cc_final: 0.6177 (tm-30) REVERT: B 122 LYS cc_start: 0.7643 (pttt) cc_final: 0.7184 (pttm) REVERT: B 164 MET cc_start: 0.8161 (ttt) cc_final: 0.7822 (ttt) REVERT: B 280 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7783 (mp10) REVERT: B 383 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 406 MET cc_start: 0.7088 (tpp) cc_final: 0.6639 (tpp) REVERT: E 22 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: E 41 ASP cc_start: 0.7347 (t0) cc_final: 0.7108 (t0) REVERT: E 86 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7533 (ttp-110) REVERT: E 88 ASP cc_start: 0.7540 (t0) cc_final: 0.7108 (t0) REVERT: E 114 ASP cc_start: 0.7712 (m-30) cc_final: 0.7416 (m-30) REVERT: E 298 ASN cc_start: 0.8287 (t0) cc_final: 0.7931 (t0) REVERT: E 344 TRP cc_start: 0.8483 (p-90) cc_final: 0.8265 (p-90) REVERT: E 362 LYS cc_start: 0.7609 (mmtm) cc_final: 0.6829 (ttpt) REVERT: E 383 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7735 (tm-30) REVERT: E 415 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8017 (mtp) REVERT: A 24 TYR cc_start: 0.8405 (m-10) cc_final: 0.8034 (m-10) REVERT: A 49 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.5379 (t80) REVERT: A 172 TYR cc_start: 0.7949 (t80) cc_final: 0.6728 (t80) REVERT: A 280 LYS cc_start: 0.5605 (mmtt) cc_final: 0.4777 (tptp) REVERT: A 313 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7653 (ptm) REVERT: A 386 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7823 (mm-30) REVERT: D 1 MET cc_start: 0.2802 (OUTLIER) cc_final: 0.2429 (tmm) REVERT: D 214 ARG cc_start: 0.8263 (ttm170) cc_final: 0.7920 (ttm110) REVERT: D 279 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7778 (mp0) REVERT: D 326 LYS cc_start: 0.8794 (tttt) cc_final: 0.7636 (mptm) REVERT: D 390 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7422 (ttp80) REVERT: D 392 ASP cc_start: 0.8143 (m-30) cc_final: 0.7910 (m-30) REVERT: D 433 GLU cc_start: 0.7917 (tp30) cc_final: 0.7580 (tp30) outliers start: 63 outliers final: 20 residues processed: 289 average time/residue: 0.6700 time to fit residues: 210.7417 Evaluate side-chains 226 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 375 GLN Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 429 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 298 ASN B 307 HIS E 8 GLN E 28 HIS E 424 GLN A 128 GLN A 309 HIS D 15 GLN D 309 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099751 restraints weight = 19724.680| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.71 r_work: 0.3322 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13890 Z= 0.215 Angle : 0.630 8.706 18889 Z= 0.327 Chirality : 0.047 0.205 2078 Planarity : 0.005 0.066 2463 Dihedral : 11.459 173.678 1925 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.05 % Allowed : 16.12 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.42 (0.20), residues: 1720 helix: 1.23 (0.18), residues: 812 sheet: -0.35 (0.32), residues: 266 loop : -0.57 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 213 TYR 0.018 0.002 TYR D 24 PHE 0.019 0.002 PHE D 149 TRP 0.011 0.002 TRP D 388 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00507 (13890) covalent geometry : angle 0.62977 (18889) hydrogen bonds : bond 0.05235 ( 678) hydrogen bonds : angle 4.88431 ( 2007) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 0.548 Fit side-chains REVERT: B 15 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: B 41 ASP cc_start: 0.7042 (t0) cc_final: 0.6809 (t0) REVERT: B 44 LEU cc_start: 0.8476 (mt) cc_final: 0.8216 (mp) REVERT: B 280 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7800 (mp10) REVERT: B 343 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7406 (pm20) REVERT: B 361 LEU cc_start: 0.5117 (OUTLIER) cc_final: 0.4808 (mt) REVERT: B 383 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7719 (tm-30) REVERT: B 406 MET cc_start: 0.7387 (tpp) cc_final: 0.7016 (tpp) REVERT: E 22 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: E 86 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7905 (ttp-110) REVERT: E 383 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7763 (tm-30) REVERT: E 392 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8789 (mtpt) REVERT: A 24 TYR cc_start: 0.8503 (m-10) cc_final: 0.8084 (m-10) REVERT: A 49 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.5094 (t80) REVERT: A 55 GLU cc_start: 0.8085 (tp30) cc_final: 0.7866 (tp30) REVERT: A 172 TYR cc_start: 0.7960 (t80) cc_final: 0.7678 (t80) REVERT: A 214 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8411 (ttp-110) REVERT: A 272 TYR cc_start: 0.8904 (t80) cc_final: 0.8615 (t80) REVERT: A 279 GLU cc_start: 0.7873 (mp0) cc_final: 0.7566 (mp0) REVERT: A 280 LYS cc_start: 0.5988 (mmtt) cc_final: 0.5005 (tptt) REVERT: A 285 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7459 (tp40) REVERT: A 386 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7963 (mm-30) REVERT: D 1 MET cc_start: 0.2141 (OUTLIER) cc_final: 0.1801 (tmm) REVERT: D 254 GLU cc_start: 0.4878 (mm-30) cc_final: 0.4295 (mm-30) REVERT: D 326 LYS cc_start: 0.9027 (tttt) cc_final: 0.7755 (mmtp) REVERT: D 384 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8857 (tp) REVERT: D 390 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7608 (ttp80) REVERT: D 392 ASP cc_start: 0.8269 (m-30) cc_final: 0.8002 (m-30) outliers start: 73 outliers final: 29 residues processed: 254 average time/residue: 0.6521 time to fit residues: 180.6734 Evaluate side-chains 225 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 429 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 0.0980 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 129 optimal weight: 0.2980 chunk 89 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 132 optimal weight: 0.1980 overall best weight: 0.1496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS E 247 ASN ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN E 426 GLN A 15 GLN A 128 GLN A 216 ASN A 300 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103843 restraints weight = 19412.728| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.79 r_work: 0.3381 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13890 Z= 0.115 Angle : 0.519 8.750 18889 Z= 0.267 Chirality : 0.042 0.164 2078 Planarity : 0.004 0.081 2463 Dihedral : 11.054 177.207 1923 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.32 % Allowed : 19.03 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.72 (0.21), residues: 1720 helix: 1.53 (0.18), residues: 814 sheet: -0.26 (0.32), residues: 272 loop : -0.49 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 214 TYR 0.014 0.001 TYR D 24 PHE 0.012 0.001 PHE D 149 TRP 0.011 0.001 TRP E 344 HIS 0.003 0.001 HIS E 396 Details of bonding type rmsd covalent geometry : bond 0.00241 (13890) covalent geometry : angle 0.51869 (18889) hydrogen bonds : bond 0.04111 ( 678) hydrogen bonds : angle 4.58150 ( 2007) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.522 Fit side-chains REVERT: B 3 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: B 267 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7669 (ptp) REVERT: B 280 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7886 (mp10) REVERT: B 343 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7304 (pm20) REVERT: B 361 LEU cc_start: 0.4817 (OUTLIER) cc_final: 0.4597 (mt) REVERT: B 383 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 406 MET cc_start: 0.7375 (tpp) cc_final: 0.7016 (tpp) REVERT: E 22 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: E 122 LYS cc_start: 0.8166 (pttm) cc_final: 0.7687 (ptmm) REVERT: E 282 ARG cc_start: 0.5762 (ptm160) cc_final: 0.5473 (ptm160) REVERT: E 288 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7139 (tp30) REVERT: E 383 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7659 (tm-30) REVERT: A 24 TYR cc_start: 0.8411 (m-10) cc_final: 0.8044 (m-10) REVERT: A 35 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: A 49 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5166 (t80) REVERT: A 73 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8007 (m) REVERT: A 161 TYR cc_start: 0.8586 (m-80) cc_final: 0.8351 (m-80) REVERT: A 172 TYR cc_start: 0.7727 (t80) cc_final: 0.6841 (t80) REVERT: A 272 TYR cc_start: 0.8766 (t80) cc_final: 0.8478 (t80) REVERT: A 279 GLU cc_start: 0.8118 (mp0) cc_final: 0.7657 (mp0) REVERT: A 280 LYS cc_start: 0.5924 (mmtt) cc_final: 0.4938 (tptt) REVERT: A 386 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7927 (mm-30) REVERT: D 1 MET cc_start: 0.2033 (OUTLIER) cc_final: 0.1682 (tmm) REVERT: D 326 LYS cc_start: 0.9012 (tttt) cc_final: 0.7858 (mptt) REVERT: D 392 ASP cc_start: 0.8150 (m-30) cc_final: 0.7927 (m-30) outliers start: 48 outliers final: 13 residues processed: 230 average time/residue: 0.6445 time to fit residues: 162.1954 Evaluate side-chains 214 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 413 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1111 > 50: distance: 50 - 56: 3.129 distance: 51 - 84: 10.717 distance: 57 - 58: 4.764 distance: 57 - 60: 5.658 distance: 58 - 59: 12.830 distance: 58 - 64: 3.477 distance: 59 - 92: 8.814 distance: 60 - 61: 4.059 distance: 61 - 62: 8.720 distance: 61 - 63: 9.248 distance: 64 - 65: 9.570 distance: 65 - 66: 8.451 distance: 65 - 68: 9.408 distance: 66 - 67: 8.777 distance: 66 - 75: 11.916 distance: 67 - 97: 32.849 distance: 68 - 69: 14.478 distance: 69 - 70: 3.385 distance: 71 - 72: 5.039 distance: 72 - 73: 19.857 distance: 72 - 74: 10.279 distance: 75 - 76: 8.566 distance: 76 - 77: 5.401 distance: 76 - 79: 3.364 distance: 77 - 78: 11.550 distance: 77 - 84: 4.194 distance: 78 - 104: 4.432 distance: 79 - 80: 21.890 distance: 80 - 81: 11.385 distance: 81 - 82: 3.963 distance: 82 - 83: 31.719 distance: 84 - 85: 3.595 distance: 85 - 86: 9.723 distance: 85 - 88: 4.049 distance: 86 - 87: 7.623 distance: 86 - 92: 7.834 distance: 87 - 112: 19.029 distance: 88 - 89: 9.294 distance: 89 - 90: 6.393 distance: 89 - 91: 7.644 distance: 92 - 93: 10.664 distance: 93 - 94: 12.711 distance: 93 - 96: 6.134 distance: 94 - 95: 9.672 distance: 94 - 97: 15.495 distance: 95 - 120: 12.709 distance: 97 - 98: 4.147 distance: 98 - 99: 11.810 distance: 98 - 101: 15.337 distance: 99 - 100: 7.677 distance: 99 - 104: 3.249 distance: 101 - 102: 16.895 distance: 101 - 103: 26.164 distance: 104 - 105: 3.976 distance: 105 - 106: 7.514 distance: 105 - 108: 8.691 distance: 106 - 107: 9.607 distance: 108 - 109: 9.793 distance: 109 - 110: 18.655 distance: 109 - 111: 27.087 distance: 112 - 113: 3.880 distance: 113 - 114: 8.448 distance: 113 - 116: 12.541 distance: 114 - 115: 17.351 distance: 114 - 120: 6.197 distance: 116 - 117: 13.713 distance: 117 - 118: 18.148 distance: 118 - 119: 17.954 distance: 120 - 121: 5.507 distance: 121 - 122: 8.813 distance: 121 - 124: 15.678 distance: 122 - 123: 28.967 distance: 122 - 127: 22.251 distance: 124 - 125: 17.585 distance: 124 - 126: 11.202 distance: 127 - 128: 36.624 distance: 127 - 133: 47.750 distance: 128 - 129: 13.071 distance: 128 - 131: 4.283 distance: 129 - 130: 11.968 distance: 129 - 134: 29.153 distance: 131 - 132: 39.454 distance: 132 - 133: 8.991