Starting phenix.real_space_refine on Sat Aug 23 21:41:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bti_30179/08_2025/7bti_30179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bti_30179/08_2025/7bti_30179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bti_30179/08_2025/7bti_30179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bti_30179/08_2025/7bti_30179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bti_30179/08_2025/7bti_30179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bti_30179/08_2025/7bti_30179.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 5 5.21 5 S 108 5.16 5 C 9239 2.51 5 N 2475 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 14650 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2855 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "C" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2868 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2862 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "X" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'G5G:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.71, per 1000 atoms: 0.32 Number of scatterers: 14650 At special positions: 0 Unit cell: (95.22, 95.22, 193.2, 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 108 16.00 P 10 15.00 Mg 5 11.99 O 2813 8.00 N 2475 7.00 C 9239 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 685.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 30 sheets defined 40.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.579A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 95 removed outlier: 4.046A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.195A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.657A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.698A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.792A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.598A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.523A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 273 through 284 removed outlier: 4.106A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 308 through 318 removed outlier: 4.015A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.981A pdb=" N GLN A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.685A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.829A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 79 through 91 removed outlier: 4.125A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.142A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.949A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.627A pdb=" N LEU B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.822A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.679A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.943A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.721A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 311 Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.057A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.699A pdb=" N ASP B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.558A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.877A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 61' Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.665A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.515A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.425A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 removed outlier: 3.642A pdb=" N LEU C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.647A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.683A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.515A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.800A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.075A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 311 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.684A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 4.007A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.777A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.520A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.531A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.208A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.546A pdb=" N LEU D 140 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.534A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.674A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 removed outlier: 3.563A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.378A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.565A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 removed outlier: 4.162A pdb=" N SER D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 4.152A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.859A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.587A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.067A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.797A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.298A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.640A pdb=" N GLN E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 91 removed outlier: 4.122A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.855A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.619A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 removed outlier: 3.882A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.644A pdb=" N TYR E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.773A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 257 through 261 removed outlier: 3.764A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.652A pdb=" N PHE E 266 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.973A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 318 removed outlier: 3.506A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 373 removed outlier: 4.199A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.665A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.534A pdb=" N VAL A 35 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 4.107A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.589A pdb=" N ASN A 162 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.551A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 41 through 42 removed outlier: 4.178A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.826A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.573A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 8 through 9 removed outlier: 6.720A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.299A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.520A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 179 Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.558A pdb=" N LYS D 238 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 250 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.514A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.797A pdb=" N LYS E 68 " --> pdb=" O VAL E 35 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'E' and resid 150 through 151 Processing sheet with id=AD1, first strand: chain 'E' and resid 160 through 161 Processing sheet with id=AD2, first strand: chain 'E' and resid 240 through 242 removed outlier: 3.852A pdb=" N GLN E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 297 through 298 removed outlier: 5.983A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 511 hydrogen bonds defined for protein. 1350 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: 2.39 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2443 1.30 - 1.43: 3806 1.43 - 1.56: 8510 1.56 - 1.68: 21 1.68 - 1.81: 189 Bond restraints: 14969 Sorted by residual: bond pdb=" C1' ADP D 402 " pdb=" C2' ADP D 402 " ideal model delta sigma weight residual 1.524 1.295 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1' ADP E 402 " pdb=" C2' ADP E 402 " ideal model delta sigma weight residual 1.524 1.295 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1' ADP C 402 " pdb=" C2' ADP C 402 " ideal model delta sigma weight residual 1.524 1.296 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP A 402 " pdb=" C2' ADP A 402 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1' ADP B 402 " pdb=" C2' ADP B 402 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 14964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 19825 2.17 - 4.35: 395 4.35 - 6.52: 50 6.52 - 8.69: 23 8.69 - 10.86: 26 Bond angle restraints: 20319 Sorted by residual: angle pdb=" C GLY C 308 " pdb=" N ILE C 309 " pdb=" CA ILE C 309 " ideal model delta sigma weight residual 121.97 131.32 -9.35 1.80e+00 3.09e-01 2.70e+01 angle pdb=" C GLY E 308 " pdb=" N ILE E 309 " pdb=" CA ILE E 309 " ideal model delta sigma weight residual 121.97 131.14 -9.17 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C GLY B 308 " pdb=" N ILE B 309 " pdb=" CA ILE B 309 " ideal model delta sigma weight residual 121.97 131.11 -9.14 1.80e+00 3.09e-01 2.58e+01 angle pdb=" N HYP X 1 " pdb=" CA HYP X 1 " pdb=" CB HYP X 1 " ideal model delta sigma weight residual 103.00 108.56 -5.56 1.10e+00 8.26e-01 2.55e+01 angle pdb=" N HYP Z 1 " pdb=" CA HYP Z 1 " pdb=" CB HYP Z 1 " ideal model delta sigma weight residual 103.00 108.45 -5.45 1.10e+00 8.26e-01 2.46e+01 ... (remaining 20314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.53: 8489 27.53 - 55.07: 468 55.07 - 82.60: 53 82.60 - 110.13: 8 110.13 - 137.66: 10 Dihedral angle restraints: 9028 sinusoidal: 3658 harmonic: 5370 Sorted by residual: dihedral pdb=" O2A ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PA ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 77.67 -137.66 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2A ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PA ADP C 402 " pdb=" PB ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 77.62 -137.62 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2A ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PA ADP E 402 " pdb=" PB ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 75.56 -135.56 1 2.00e+01 2.50e-03 4.11e+01 ... (remaining 9025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2242 0.143 - 0.287: 18 0.287 - 0.430: 0 0.430 - 0.574: 0 0.574 - 0.717: 3 Chirality restraints: 2263 Sorted by residual: chirality pdb=" CA G5G X 4 " pdb=" N G5G X 4 " pdb=" C G5G X 4 " pdb=" CB G5G X 4 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA G5G Z 4 " pdb=" N G5G Z 4 " pdb=" C G5G Z 4 " pdb=" CB G5G Z 4 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA G5G Y 4 " pdb=" N G5G Y 4 " pdb=" C G5G Y 4 " pdb=" CB G5G Y 4 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 2260 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 306 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO E 307 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 307 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 307 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO D 243 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO B 112 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.033 5.00e-02 4.00e+02 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 243 2.65 - 3.21: 12209 3.21 - 3.77: 22506 3.77 - 4.34: 31095 4.34 - 4.90: 52487 Nonbonded interactions: 118540 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O2B ADP B 402 " model vdw 2.083 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2B ADP D 402 " model vdw 2.098 2.170 nonbonded pdb="MG MG E 401 " pdb=" O2B ADP E 402 " model vdw 2.109 2.170 nonbonded pdb="MG MG A 401 " pdb=" O3B ADP A 402 " model vdw 2.126 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3B ADP C 402 " model vdw 2.127 2.170 ... (remaining 118535 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 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 402)) selection = (chain 'B' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 212 or ( \ resid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 232 or resid 236 through 308 or (resid 309 through 310 and (name N or na \ me CA or name C or name O or name CB )) or resid 311 through 402)) selection = (chain 'C' and (resid 6 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 232 or resid 236 through 308 or \ (resid 309 through 310 and (name N or name CA or name C or name O or name CB )) \ or resid 311 through 402)) selection = (chain 'D' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 212 or ( \ resid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 232 or resid 236 through 308 or (resid 309 through 310 and (name N or na \ me CA or name C or name O or name CB )) or resid 311 through 402)) selection = (chain 'E' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 212 or ( \ resid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 308 or (resid 309 through 310 and (name N or name CA or name C or name O \ or name CB )) or resid 311 through 402)) } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 group one per residue 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.430 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.010 0.231 14972 Z= 0.492 Angle : 0.858 10.863 20319 Z= 0.439 Chirality : 0.057 0.717 2263 Planarity : 0.007 0.068 2586 Dihedral : 17.054 137.664 5588 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.70 % Favored : 94.08 % Rotamer: Outliers : 10.93 % Allowed : 11.06 % Favored : 78.01 % 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 aren not related in a simple way. whole: -4.46 (0.16), residues: 1825 helix: -3.24 (0.13), residues: 687 sheet: -3.03 (0.24), residues: 312 loop : -2.51 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 206 TYR 0.012 0.001 TYR C 143 PHE 0.015 0.002 PHE E 255 TRP 0.010 0.002 TRP E 340 HIS 0.005 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.01016 (14969) covalent geometry : angle 0.85806 (20319) hydrogen bonds : bond 0.20856 ( 511) hydrogen bonds : angle 8.02602 ( 1350) Misc. bond : bond 0.03203 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 116 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8615 (tpp) cc_final: 0.8366 (tpt) REVERT: A 291 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8704 (mptt) REVERT: A 311 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8035 (t0) REVERT: A 313 MET cc_start: 0.8224 (mmm) cc_final: 0.8016 (mmm) REVERT: A 369 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8238 (tt) REVERT: B 49 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: B 62 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.7741 (ptt180) REVERT: B 291 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8177 (mmtt) REVERT: B 328 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8144 (tttm) REVERT: B 335 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8716 (ptp-170) REVERT: C 136 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9257 (tt) REVERT: C 195 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.6894 (pp20) REVERT: D 50 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7441 (ttpp) REVERT: D 140 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9122 (mt) REVERT: D 194 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9078 (p) REVERT: D 260 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8865 (p) REVERT: E 12 ASN cc_start: 0.8865 (t0) cc_final: 0.8532 (p0) REVERT: E 44 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8452 (mpt) REVERT: E 103 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8966 (m) REVERT: E 227 MET cc_start: 0.8545 (mmm) cc_final: 0.8261 (mmm) outliers start: 170 outliers final: 55 residues processed: 280 average time/residue: 0.1059 time to fit residues: 45.3960 Evaluate side-chains 160 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 89 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0040 overall best weight: 0.7234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 137 GLN A 161 HIS A 353 GLN A 354 GLN B 49 GLN B 111 ASN B 115 ASN B 162 ASN B 246 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 246 GLN C 314 GLN D 88 HIS D 92 ASN D 115 ASN D 137 GLN D 161 HIS D 246 GLN D 314 GLN E 162 ASN E 314 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.056842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.048021 restraints weight = 43395.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.049546 restraints weight = 22079.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.050545 restraints weight = 13813.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.051180 restraints weight = 9948.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.051644 restraints weight = 8020.039| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14972 Z= 0.105 Angle : 0.631 7.939 20319 Z= 0.306 Chirality : 0.044 0.203 2263 Planarity : 0.005 0.051 2586 Dihedral : 13.825 139.477 2269 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.57 % Allowed : 14.60 % Favored : 80.84 % 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 aren not related in a simple way. whole: -3.10 (0.18), residues: 1825 helix: -1.92 (0.17), residues: 684 sheet: -2.25 (0.25), residues: 332 loop : -1.92 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 372 TYR 0.008 0.001 TYR C 69 PHE 0.008 0.001 PHE E 255 TRP 0.008 0.001 TRP E 340 HIS 0.005 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00230 (14969) covalent geometry : angle 0.63060 (20319) hydrogen bonds : bond 0.03493 ( 511) hydrogen bonds : angle 5.62084 ( 1350) Misc. bond : bond 0.00096 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 99 time to evaluate : 0.595 Fit side-chains REVERT: A 291 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8661 (mptt) REVERT: A 320 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8854 (pp) REVERT: B 328 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8185 (tttm) REVERT: C 136 ILE cc_start: 0.9534 (OUTLIER) cc_final: 0.9190 (tt) REVERT: C 195 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.6998 (pp20) REVERT: D 50 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6763 (tttm) REVERT: D 132 MET cc_start: 0.8460 (ptm) cc_final: 0.8151 (tmm) REVERT: D 141 SER cc_start: 0.9381 (OUTLIER) cc_final: 0.9084 (t) REVERT: D 289 ILE cc_start: 0.9154 (mp) cc_final: 0.8883 (mm) REVERT: E 12 ASN cc_start: 0.8765 (t0) cc_final: 0.8267 (p0) REVERT: E 140 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8900 (mp) REVERT: E 176 MET cc_start: 0.8750 (mmm) cc_final: 0.8439 (mmt) REVERT: E 227 MET cc_start: 0.8511 (mmm) cc_final: 0.8212 (mmm) REVERT: E 305 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7971 (mmt) outliers start: 71 outliers final: 37 residues processed: 164 average time/residue: 0.0977 time to fit residues: 25.1821 Evaluate side-chains 138 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 143 optimal weight: 0.0970 chunk 37 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 137 GLN C 161 HIS D 115 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.047051 restraints weight = 44145.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.048582 restraints weight = 22376.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.049575 restraints weight = 13976.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.050236 restraints weight = 10082.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.050629 restraints weight = 8017.596| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14972 Z= 0.163 Angle : 0.623 7.150 20319 Z= 0.301 Chirality : 0.045 0.178 2263 Planarity : 0.004 0.047 2586 Dihedral : 12.653 139.069 2202 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.24 % Allowed : 15.11 % Favored : 80.64 % 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 aren not related in a simple way. whole: -2.51 (0.19), residues: 1825 helix: -1.34 (0.19), residues: 705 sheet: -1.89 (0.26), residues: 332 loop : -1.71 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.009 0.001 TYR C 53 PHE 0.007 0.001 PHE B 262 TRP 0.009 0.001 TRP E 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00375 (14969) covalent geometry : angle 0.62253 (20319) hydrogen bonds : bond 0.03263 ( 511) hydrogen bonds : angle 5.27974 ( 1350) Misc. bond : bond 0.00051 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 92 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7469 (pmm) cc_final: 0.7096 (tpt) REVERT: A 291 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8687 (mptt) REVERT: A 320 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8961 (pp) REVERT: B 328 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8096 (tttm) REVERT: C 16 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8990 (mt) REVERT: C 51 ASP cc_start: 0.6141 (OUTLIER) cc_final: 0.5894 (m-30) REVERT: C 136 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9194 (tt) REVERT: C 195 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7073 (pp20) REVERT: D 50 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6906 (tttm) REVERT: D 289 ILE cc_start: 0.9113 (mp) cc_final: 0.8826 (mm) REVERT: D 330 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8579 (pp) REVERT: E 12 ASN cc_start: 0.8808 (t0) cc_final: 0.8149 (p0) REVERT: E 45 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8051 (t) REVERT: E 140 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9003 (mp) REVERT: E 176 MET cc_start: 0.8736 (mmm) cc_final: 0.8405 (mmt) REVERT: E 227 MET cc_start: 0.8500 (mmm) cc_final: 0.8200 (mmm) REVERT: E 305 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8010 (mmt) outliers start: 66 outliers final: 41 residues processed: 155 average time/residue: 0.0851 time to fit residues: 21.3324 Evaluate side-chains 143 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 90 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 12 ASN C 88 HIS D 162 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.054806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.045942 restraints weight = 44499.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.047442 restraints weight = 22869.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.048420 restraints weight = 14363.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.049059 restraints weight = 10435.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.049528 restraints weight = 8361.857| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14972 Z= 0.235 Angle : 0.660 7.515 20319 Z= 0.320 Chirality : 0.047 0.177 2263 Planarity : 0.004 0.051 2586 Dihedral : 12.313 138.061 2197 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.69 % Allowed : 14.92 % Favored : 80.39 % 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 aren not related in a simple way. whole: -2.27 (0.19), residues: 1825 helix: -1.15 (0.19), residues: 696 sheet: -1.70 (0.26), residues: 337 loop : -1.58 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.010 0.001 TYR C 69 PHE 0.010 0.001 PHE D 266 TRP 0.012 0.002 TRP E 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00545 (14969) covalent geometry : angle 0.66001 (20319) hydrogen bonds : bond 0.03362 ( 511) hydrogen bonds : angle 5.30330 ( 1350) Misc. bond : bond 0.00057 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 89 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7828 (pmm) cc_final: 0.7081 (tpt) REVERT: A 291 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8676 (mptt) REVERT: A 320 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8998 (pp) REVERT: B 328 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8140 (tttm) REVERT: C 16 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9027 (mt) REVERT: C 51 ASP cc_start: 0.6313 (OUTLIER) cc_final: 0.6061 (m-30) REVERT: C 136 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9188 (tt) REVERT: C 195 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7184 (pp20) REVERT: D 227 MET cc_start: 0.8183 (mmm) cc_final: 0.7879 (mmm) REVERT: D 313 MET cc_start: 0.7818 (mmm) cc_final: 0.7300 (mtp) REVERT: D 330 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (pp) REVERT: E 12 ASN cc_start: 0.8792 (t0) cc_final: 0.8152 (p0) REVERT: E 45 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8099 (t) REVERT: E 140 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9021 (mp) REVERT: E 176 MET cc_start: 0.8661 (mmm) cc_final: 0.8314 (mmt) REVERT: E 227 MET cc_start: 0.8317 (mmm) cc_final: 0.7990 (mmm) REVERT: E 275 HIS cc_start: 0.9067 (OUTLIER) cc_final: 0.7697 (p-80) REVERT: E 305 MET cc_start: 0.8434 (mtp) cc_final: 0.8028 (mmm) REVERT: E 325 MET cc_start: 0.7637 (ttm) cc_final: 0.7312 (ttm) outliers start: 73 outliers final: 43 residues processed: 158 average time/residue: 0.0891 time to fit residues: 22.7486 Evaluate side-chains 142 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 88 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 369 ILE 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: 53.4822 > 50: distance: 47 - 48: 5.798 distance: 47 - 50: 4.205 distance: 48 - 55: 5.307 distance: 50 - 51: 8.236 distance: 51 - 52: 5.758 distance: 52 - 53: 3.879 distance: 52 - 54: 5.490 distance: 55 - 56: 3.071 distance: 56 - 57: 9.201 distance: 56 - 59: 7.686 distance: 57 - 66: 5.103 distance: 59 - 60: 5.487 distance: 60 - 61: 4.004 distance: 61 - 62: 5.706 distance: 62 - 63: 4.418 distance: 63 - 64: 6.319 distance: 63 - 65: 6.841 distance: 66 - 67: 4.527 distance: 67 - 68: 5.620 distance: 68 - 69: 12.203 distance: 68 - 70: 15.296 distance: 70 - 71: 21.493 distance: 71 - 72: 20.139 distance: 71 - 74: 8.026 distance: 72 - 73: 20.808 distance: 72 - 82: 9.578 distance: 74 - 75: 5.960 distance: 75 - 76: 5.157 distance: 76 - 78: 4.240 distance: 77 - 79: 5.033 distance: 78 - 80: 3.094 distance: 79 - 80: 5.569 distance: 80 - 81: 8.883 distance: 82 - 83: 6.187 distance: 83 - 84: 15.102 distance: 83 - 86: 11.925 distance: 84 - 85: 18.072 distance: 89 - 90: 7.576 distance: 89 - 92: 5.178 distance: 90 - 91: 3.580 distance: 93 - 95: 4.901 distance: 96 - 98: 3.865 distance: 97 - 98: 4.486 distance: 99 - 100: 3.570 distance: 101 - 102: 8.448 distance: 101 - 106: 4.881 distance: 103 - 104: 5.195 distance: 103 - 105: 8.608 distance: 107 - 108: 3.126 distance: 107 - 110: 5.006 distance: 108 - 109: 4.690 distance: 108 - 113: 4.598 distance: 109 - 134: 11.833 distance: 110 - 111: 9.423 distance: 110 - 112: 8.385 distance: 114 - 115: 3.287 distance: 115 - 116: 3.463 distance: 116 - 141: 6.163 distance: 120 - 121: 3.164 distance: 121 - 122: 5.490 distance: 121 - 124: 4.534 distance: 122 - 125: 3.150