Starting phenix.real_space_refine on Sat Sep 12 08:55:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bti_30179/09_2026/7bti_30179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bti_30179/09_2026/7bti_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_30179/09_2026/7bti_30179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bti_30179/09_2026/7bti_30179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bti_30179/09_2026/7bti_30179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bti_30179/09_2026/7bti_30179.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bti_30179/09_2026/7bti_30179.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bti_30179/09_2026/7bti_30179.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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: 3.47, per 1000 atoms: 0.24 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: 1.14 Conformation dependent library (CDL) restraints added in 612.1 milliseconds 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: 0.49 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: 2.31 Time building geometry restraints manager: 1.52 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: 8468 27.53 - 55.07: 455 55.07 - 82.60: 39 82.60 - 110.13: 8 110.13 - 137.66: 10 Dihedral angle restraints: 8980 sinusoidal: 3610 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 8977 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: 1.230 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 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 : 16.588 137.664 5540 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 are 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/Z covalent geometry : bond 0.01016 / 0.49 (14969) covalent geometry : angle 0.85806 / 0.44 (20319) hydrogen bonds : bond 0.20856 / 14.05 ( 511) hydrogen bonds : angle 8.02602 / 5.71 ( 1350) Misc. bond : bond 0.03203 / 1.49 ( 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 : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8615 (tpp) cc_final: 0.8371 (tpt) REVERT: A 291 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8705 (mptt) REVERT: A 311 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8034 (t0) REVERT: A 313 MET cc_start: 0.8224 (mmm) cc_final: 0.8015 (mmm) REVERT: A 369 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8230 (tt) REVERT: B 49 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: B 62 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.7742 (ptt180) REVERT: B 180 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (tt) REVERT: B 291 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8178 (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: 0.8717 (ptp-170) REVERT: C 51 ASP cc_start: 0.6254 (OUTLIER) cc_final: 0.6053 (m-30) REVERT: C 195 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: C 370 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.9001 (p) 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: 0.9123 (mt) REVERT: D 194 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9079 (p) REVERT: D 260 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8866 (p) REVERT: E 12 ASN cc_start: 0.8865 (t0) cc_final: 0.8534 (p0) REVERT: E 44 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8451 (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: 0.8263 (mmm) outliers start: 170 outliers final: 55 residues processed: 280 average time/residue: 0.1091 time to fit residues: 47.2365 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 : 0.491 ------------------------------------------------------------------------------- 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 180 LEU 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 51 ASP Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 134 VAL 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 C residue 370 VAL 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: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0040 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 137 GLN 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 111 ASN E 162 ASN E 314 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.056145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.047359 restraints weight = 43571.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.048879 restraints weight = 22250.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.049873 restraints weight = 13913.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.050520 restraints weight = 10030.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.050977 restraints weight = 8016.587| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14972 Z= 0.132 Angle : 0.642 7.600 20319 Z= 0.315 Chirality : 0.045 0.184 2263 Planarity : 0.005 0.051 2586 Dihedral : 12.843 138.391 2224 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.63 % Allowed : 15.05 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.18), residues: 1825 helix: -1.94 (0.17), residues: 684 sheet: -2.29 (0.25), residues: 332 loop : -1.94 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 372 TYR 0.008 0.001 TYR C 69 PHE 0.008 0.001 PHE E 255 TRP 0.010 0.001 TRP E 340 HIS 0.005 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14969) covalent geometry : angle 0.64221 / 0.31 (20319) hydrogen bonds : bond 0.03739 / 2.53 ( 511) hydrogen bonds : angle 5.64809 / 4.02 ( 1350) Misc. bond : bond 0.00036 / 0.02 ( 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 171 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 99 time to evaluate : 0.644 Fit side-chains REVERT: A 291 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8663 (mptt) REVERT: A 320 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8878 (pp) REVERT: B 328 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8191 (tttm) REVERT: C 195 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7043 (pp20) REVERT: C 370 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8983 (p) REVERT: D 50 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6880 (tttm) REVERT: D 141 SER cc_start: 0.9407 (OUTLIER) cc_final: 0.9087 (t) REVERT: E 12 ASN cc_start: 0.8768 (t0) cc_final: 0.8265 (p0) REVERT: E 176 MET cc_start: 0.8753 (mmm) cc_final: 0.8388 (mmt) REVERT: E 227 MET cc_start: 0.8500 (mmm) cc_final: 0.8204 (mmm) REVERT: E 305 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7971 (mmm) outliers start: 72 outliers final: 39 residues processed: 166 average time/residue: 0.1050 time to fit residues: 27.6413 Evaluate side-chains 138 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 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 C residue 370 VAL 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 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 303 THR 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: 9.9990 chunk 57 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 115 ASN C 88 HIS C 92 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 162 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.053767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.045041 restraints weight = 44920.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.046513 restraints weight = 22992.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.047446 restraints weight = 14445.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.048083 restraints weight = 10561.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.048530 restraints weight = 8439.317| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 14972 Z= 0.336 Angle : 0.745 7.228 20319 Z= 0.368 Chirality : 0.050 0.184 2263 Planarity : 0.005 0.049 2586 Dihedral : 11.931 135.124 2154 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 4.89 % Allowed : 14.86 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.19), residues: 1825 helix: -1.66 (0.18), residues: 729 sheet: -2.02 (0.26), residues: 334 loop : -1.78 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 372 TYR 0.015 0.001 TYR D 198 PHE 0.015 0.002 PHE D 266 TRP 0.014 0.002 TRP E 340 HIS 0.005 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.34 (14969) covalent geometry : angle 0.74454 / 0.37 (20319) hydrogen bonds : bond 0.04079 / 2.80 ( 511) hydrogen bonds : angle 5.60625 / 3.98 ( 1350) Misc. bond : bond 0.00065 / 0.03 ( 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 164 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 88 time to evaluate : 0.558 Fit side-chains REVERT: A 291 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8681 (mptt) REVERT: A 320 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9013 (pp) REVERT: B 328 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8135 (tttm) REVERT: C 16 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9042 (mt) REVERT: C 51 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5991 (m-30) REVERT: C 195 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7184 (pp20) REVERT: C 287 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8381 (mt) REVERT: C 325 MET cc_start: 0.8494 (mmt) cc_final: 0.8226 (tpt) REVERT: D 141 SER cc_start: 0.9361 (OUTLIER) cc_final: 0.9072 (t) REVERT: D 227 MET cc_start: 0.8187 (mmm) cc_final: 0.7847 (mmm) REVERT: D 330 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8558 (pp) REVERT: E 12 ASN cc_start: 0.8825 (t0) cc_final: 0.8249 (p0) REVERT: E 176 MET cc_start: 0.8676 (mmm) cc_final: 0.8248 (mmt) REVERT: E 227 MET cc_start: 0.8373 (mmm) cc_final: 0.8031 (mmm) REVERT: E 275 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.8015 (p-80) REVERT: E 305 MET cc_start: 0.8469 (mtp) cc_final: 0.8016 (mmm) outliers start: 76 outliers final: 44 residues processed: 162 average time/residue: 0.1006 time to fit residues: 26.1383 Evaluate side-chains 141 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 87 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 34 ILE Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 134 VAL 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 287 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 10 CYS 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 141 SER Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 0.0040 chunk 53 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN C 12 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.056533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.047767 restraints weight = 43702.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.049319 restraints weight = 21986.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.050325 restraints weight = 13657.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.050992 restraints weight = 9791.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.051440 restraints weight = 7740.009| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14972 Z= 0.103 Angle : 0.596 7.364 20319 Z= 0.286 Chirality : 0.044 0.175 2263 Planarity : 0.004 0.049 2586 Dihedral : 10.833 137.902 2147 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.99 % Allowed : 16.40 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.19), residues: 1825 helix: -1.11 (0.19), residues: 705 sheet: -1.71 (0.27), residues: 335 loop : -1.55 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.009 0.001 TYR C 69 PHE 0.010 0.001 PHE E 255 TRP 0.008 0.001 TRP A 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (14969) covalent geometry : angle 0.59631 / 0.29 (20319) hydrogen bonds : bond 0.02753 / 1.87 ( 511) hydrogen bonds : angle 5.16759 / 3.68 ( 1350) Misc. bond : bond 0.00050 / 0.02 ( 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 155 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 93 time to evaluate : 0.491 Fit side-chains REVERT: A 82 MET cc_start: 0.9272 (tpt) cc_final: 0.9066 (tpt) REVERT: A 291 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8639 (mptt) REVERT: A 320 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8870 (pp) REVERT: B 305 MET cc_start: 0.8731 (mmm) cc_final: 0.8452 (tpp) REVERT: B 328 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8110 (tttm) REVERT: C 195 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7128 (pp20) REVERT: D 50 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6660 (tmtt) REVERT: D 313 MET cc_start: 0.7698 (mmm) cc_final: 0.7305 (mtp) REVERT: E 176 MET cc_start: 0.8694 (mmm) cc_final: 0.8333 (mmt) REVERT: E 227 MET cc_start: 0.8384 (mmm) cc_final: 0.8049 (mmm) REVERT: E 305 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7972 (mmt) outliers start: 62 outliers final: 36 residues processed: 151 average time/residue: 0.0981 time to fit residues: 23.9068 Evaluate side-chains 131 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 89 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 54 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 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 267 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL 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 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 369 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 102 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.055483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.046588 restraints weight = 44148.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.048093 restraints weight = 22625.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.049094 restraints weight = 14252.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.049767 restraints weight = 10286.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.050202 restraints weight = 8190.586| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2124 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= 0.180 Angle : 0.630 9.701 20319 Z= 0.301 Chirality : 0.046 0.176 2263 Planarity : 0.004 0.052 2586 Dihedral : 10.396 136.535 2137 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.41 % Allowed : 16.91 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.19), residues: 1825 helix: -0.96 (0.20), residues: 696 sheet: -1.58 (0.27), residues: 337 loop : -1.44 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.010 0.001 TYR E 166 PHE 0.009 0.001 PHE E 255 TRP 0.009 0.001 TRP E 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (14969) covalent geometry : angle 0.62958 / 0.30 (20319) hydrogen bonds : bond 0.03018 / 2.06 ( 511) hydrogen bonds : angle 5.12266 / 3.64 ( 1350) Misc. bond : bond 0.00038 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 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 144 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 91 time to evaluate : 0.637 Fit side-chains REVERT: A 47 MET cc_start: 0.7720 (pmm) cc_final: 0.7191 (tpt) REVERT: A 180 LEU cc_start: 0.9239 (tp) cc_final: 0.9005 (tp) REVERT: A 291 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8662 (mptt) REVERT: B 305 MET cc_start: 0.8808 (mmm) cc_final: 0.8558 (tpp) REVERT: B 328 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8099 (tttm) REVERT: D 50 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6892 (tttp) REVERT: E 45 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8076 (t) REVERT: E 176 MET cc_start: 0.8684 (mmm) cc_final: 0.8312 (mmt) REVERT: E 227 MET cc_start: 0.8341 (mmm) cc_final: 0.8013 (mmm) REVERT: E 305 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8010 (mmm) outliers start: 53 outliers final: 39 residues processed: 140 average time/residue: 0.1058 time to fit residues: 23.8467 Evaluate side-chains 135 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 91 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 54 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 16 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE 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 34 ILE 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 267 ILE Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 14 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 148 optimal weight: 0.0060 chunk 152 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.054913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.046090 restraints weight = 44172.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.047590 restraints weight = 22533.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.048564 restraints weight = 14136.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.049222 restraints weight = 10261.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.049631 restraints weight = 8170.597| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14972 Z= 0.224 Angle : 0.653 8.519 20319 Z= 0.314 Chirality : 0.047 0.178 2263 Planarity : 0.004 0.052 2586 Dihedral : 10.304 136.121 2133 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.92 % Allowed : 16.78 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.19), residues: 1825 helix: -0.92 (0.20), residues: 694 sheet: -1.52 (0.27), residues: 337 loop : -1.43 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.010 0.001 TYR E 166 PHE 0.011 0.001 PHE B 262 TRP 0.010 0.001 TRP E 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (14969) covalent geometry : angle 0.65313 / 0.31 (20319) hydrogen bonds : bond 0.03116 / 2.14 ( 511) hydrogen bonds : angle 5.16106 / 3.66 ( 1350) Misc. bond : bond 0.00047 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 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 152 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 91 time to evaluate : 0.597 Fit side-chains REVERT: A 47 MET cc_start: 0.7647 (pmm) cc_final: 0.7063 (tpt) REVERT: A 132 MET cc_start: 0.8603 (tmm) cc_final: 0.8169 (tmm) REVERT: A 180 LEU cc_start: 0.9274 (tp) cc_final: 0.9007 (tp) REVERT: A 291 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8674 (mptt) REVERT: B 328 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8129 (tttm) REVERT: D 50 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.6807 (tmtt) REVERT: D 313 MET cc_start: 0.7763 (mmm) cc_final: 0.7345 (mtp) REVERT: E 45 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8089 (t) REVERT: E 176 MET cc_start: 0.8652 (mmm) cc_final: 0.8284 (mmt) REVERT: E 227 MET cc_start: 0.8267 (mmm) cc_final: 0.7998 (mmm) REVERT: E 275 HIS cc_start: 0.9073 (OUTLIER) cc_final: 0.7619 (p-80) REVERT: E 305 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8021 (mmm) REVERT: E 325 MET cc_start: 0.7095 (mtt) cc_final: 0.6720 (ttm) outliers start: 61 outliers final: 44 residues processed: 146 average time/residue: 0.1026 time to fit residues: 24.1827 Evaluate side-chains 140 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 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 134 VAL Chi-restraints excluded: chain C residue 151 ILE 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 34 ILE 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 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 287 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 14 SER 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 150 optimal weight: 0.1980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.056003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.047182 restraints weight = 43540.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.048709 restraints weight = 22107.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.049705 restraints weight = 13848.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.050369 restraints weight = 10003.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.050825 restraints weight = 7959.860| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14972 Z= 0.133 Angle : 0.603 8.140 20319 Z= 0.287 Chirality : 0.045 0.174 2263 Planarity : 0.004 0.055 2586 Dihedral : 10.010 137.443 2133 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.73 % Allowed : 17.11 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1825 helix: -0.71 (0.20), residues: 694 sheet: -1.41 (0.27), residues: 337 loop : -1.30 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.008 0.001 TYR E 166 PHE 0.009 0.001 PHE E 255 TRP 0.009 0.001 TRP E 340 HIS 0.003 0.000 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (14969) covalent geometry : angle 0.60291 / 0.29 (20319) hydrogen bonds : bond 0.02721 / 1.86 ( 511) hydrogen bonds : angle 4.99606 / 3.55 ( 1350) Misc. bond : bond 0.00041 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 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 150 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 92 time to evaluate : 0.622 Fit side-chains REVERT: A 47 MET cc_start: 0.7681 (pmm) cc_final: 0.7144 (tpt) REVERT: A 132 MET cc_start: 0.8595 (tmm) cc_final: 0.8194 (tmm) REVERT: A 180 LEU cc_start: 0.9214 (tp) cc_final: 0.9007 (tp) REVERT: A 291 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8658 (mptt) REVERT: B 305 MET cc_start: 0.8773 (mmm) cc_final: 0.8503 (tpp) REVERT: B 328 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8092 (tttm) REVERT: C 132 MET cc_start: 0.8515 (ptm) cc_final: 0.8213 (tmm) REVERT: D 50 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6660 (tttp) REVERT: D 313 MET cc_start: 0.7753 (mmm) cc_final: 0.7329 (mtp) REVERT: E 45 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8045 (t) REVERT: E 176 MET cc_start: 0.8652 (mmm) cc_final: 0.8265 (mmt) REVERT: E 227 MET cc_start: 0.8307 (mmm) cc_final: 0.8040 (mmm) REVERT: E 305 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7997 (mmm) REVERT: E 325 MET cc_start: 0.7109 (mtt) cc_final: 0.6771 (ttm) outliers start: 58 outliers final: 42 residues processed: 144 average time/residue: 0.1005 time to fit residues: 23.2690 Evaluate side-chains 137 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 90 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS 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 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 151 ILE Chi-restraints excluded: chain C residue 287 ILE 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 34 ILE 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 267 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 14 SER 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 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 283 MET 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 355 MET Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 165 optimal weight: 0.1980 chunk 105 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.056020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.047204 restraints weight = 43763.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.048732 restraints weight = 22184.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.049730 restraints weight = 13909.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.050404 restraints weight = 10038.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.050806 restraints weight = 7965.807| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14972 Z= 0.145 Angle : 0.609 8.237 20319 Z= 0.290 Chirality : 0.046 0.173 2263 Planarity : 0.004 0.054 2586 Dihedral : 9.859 136.285 2131 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.73 % Allowed : 17.36 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.20), residues: 1825 helix: -0.60 (0.20), residues: 694 sheet: -1.35 (0.27), residues: 337 loop : -1.23 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.011 0.001 TYR D 166 PHE 0.008 0.001 PHE E 255 TRP 0.009 0.001 TRP E 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (14969) covalent geometry : angle 0.60885 / 0.29 (20319) hydrogen bonds : bond 0.02758 / 1.90 ( 511) hydrogen bonds : angle 4.95764 / 3.52 ( 1350) Misc. bond : bond 0.00041 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 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 148 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 90 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7680 (pmm) cc_final: 0.7127 (tpt) REVERT: A 291 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8661 (mptt) REVERT: B 30 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8724 (p) REVERT: B 328 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8087 (tttm) REVERT: C 132 MET cc_start: 0.8523 (ptm) cc_final: 0.8216 (tmm) REVERT: D 50 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6789 (tmmm) REVERT: E 45 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8037 (t) REVERT: E 176 MET cc_start: 0.8649 (mmm) cc_final: 0.8275 (mmt) REVERT: E 227 MET cc_start: 0.8335 (mmm) cc_final: 0.8066 (mmm) REVERT: E 305 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7921 (mmm) REVERT: E 325 MET cc_start: 0.7046 (mtt) cc_final: 0.6708 (ttm) outliers start: 58 outliers final: 43 residues processed: 141 average time/residue: 0.1039 time to fit residues: 23.5666 Evaluate side-chains 137 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 88 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS 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 161 HIS 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 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 34 ILE 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 267 ILE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 14 SER 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 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 355 MET Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 85 optimal weight: 0.0970 chunk 145 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 169 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.056860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.048153 restraints weight = 43640.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.049652 restraints weight = 22549.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.050629 restraints weight = 14277.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.051285 restraints weight = 10384.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.051685 restraints weight = 8281.259| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14972 Z= 0.110 Angle : 0.586 7.757 20319 Z= 0.277 Chirality : 0.045 0.171 2263 Planarity : 0.003 0.054 2586 Dihedral : 9.577 135.055 2131 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.28 % Allowed : 17.62 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1825 helix: -0.40 (0.21), residues: 682 sheet: -1.35 (0.27), residues: 361 loop : -1.09 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.008 0.001 TYR E 166 PHE 0.008 0.001 PHE E 255 TRP 0.008 0.001 TRP E 340 HIS 0.003 0.000 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (14969) covalent geometry : angle 0.58553 / 0.28 (20319) hydrogen bonds : bond 0.02544 / 1.74 ( 511) hydrogen bonds : angle 4.82753 / 3.43 ( 1350) Misc. bond : bond 0.00041 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 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 140 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 89 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9289 (tpt) cc_final: 0.9044 (tpt) REVERT: A 291 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8642 (mptt) REVERT: B 103 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9232 (m) REVERT: B 305 MET cc_start: 0.8878 (mmm) cc_final: 0.8583 (tpp) REVERT: B 328 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8005 (tttm) REVERT: C 132 MET cc_start: 0.8456 (ptm) cc_final: 0.8178 (tmm) REVERT: D 50 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7088 (tmmm) REVERT: D 313 MET cc_start: 0.7717 (mmm) cc_final: 0.7487 (mtp) REVERT: E 45 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.7981 (t) REVERT: E 165 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8944 (mm) REVERT: E 176 MET cc_start: 0.8617 (mmm) cc_final: 0.8236 (mmt) REVERT: E 227 MET cc_start: 0.8305 (mmm) cc_final: 0.7973 (mmm) REVERT: E 305 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7826 (mmt) REVERT: E 325 MET cc_start: 0.6964 (mtt) cc_final: 0.6659 (ttm) outliers start: 51 outliers final: 39 residues processed: 135 average time/residue: 0.1002 time to fit residues: 21.7003 Evaluate side-chains 134 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 88 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 161 HIS 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 14 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU 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 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 14 SER 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 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 355 MET Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 175 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.058104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.049241 restraints weight = 42966.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.050817 restraints weight = 21633.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.051818 restraints weight = 13467.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052503 restraints weight = 9774.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.052967 restraints weight = 7745.470| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14972 Z= 0.090 Angle : 0.569 7.705 20319 Z= 0.268 Chirality : 0.044 0.169 2263 Planarity : 0.003 0.051 2586 Dihedral : 9.201 130.525 2127 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.02 % Allowed : 17.62 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1825 helix: -0.11 (0.21), residues: 664 sheet: -1.25 (0.27), residues: 361 loop : -0.94 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.007 0.001 TYR E 166 PHE 0.007 0.001 PHE E 255 TRP 0.008 0.001 TRP E 340 HIS 0.003 0.000 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (14969) covalent geometry : angle 0.56903 / 0.27 (20319) hydrogen bonds : bond 0.02356 / 1.61 ( 511) hydrogen bonds : angle 4.68710 / 3.34 ( 1350) Misc. bond : bond 0.00026 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 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 142 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9311 (tpt) cc_final: 0.9089 (tpt) REVERT: A 132 MET cc_start: 0.8583 (tmm) cc_final: 0.8291 (tmm) REVERT: A 291 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8641 (mptt) REVERT: B 103 THR cc_start: 0.9477 (OUTLIER) cc_final: 0.9250 (m) REVERT: B 132 MET cc_start: 0.8871 (ppp) cc_final: 0.8645 (tmm) REVERT: B 305 MET cc_start: 0.8840 (mmm) cc_final: 0.8474 (tpp) REVERT: C 132 MET cc_start: 0.8462 (ptm) cc_final: 0.8178 (tmm) REVERT: C 325 MET cc_start: 0.7495 (tpt) cc_final: 0.7205 (tpt) REVERT: D 50 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7157 (tmmm) REVERT: D 313 MET cc_start: 0.7707 (mmm) cc_final: 0.7325 (mtp) REVERT: D 355 MET cc_start: 0.8308 (mmm) cc_final: 0.7642 (mmm) REVERT: E 45 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.7931 (t) REVERT: E 165 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8864 (mm) REVERT: E 176 MET cc_start: 0.8640 (mmm) cc_final: 0.8250 (mmt) REVERT: E 227 MET cc_start: 0.8339 (mmm) cc_final: 0.8001 (mmm) REVERT: E 305 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7707 (mmt) REVERT: E 325 MET cc_start: 0.6912 (mtt) cc_final: 0.6664 (ttm) outliers start: 47 outliers final: 35 residues processed: 136 average time/residue: 0.1052 time to fit residues: 23.1712 Evaluate side-chains 130 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE 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 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 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 14 SER 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 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 355 MET Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.056026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.047121 restraints weight = 43671.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.048650 restraints weight = 22241.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.049646 restraints weight = 14009.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.050303 restraints weight = 10157.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.050760 restraints weight = 8113.696| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14972 Z= 0.183 Angle : 0.623 7.342 20319 Z= 0.297 Chirality : 0.046 0.173 2263 Planarity : 0.004 0.054 2586 Dihedral : 9.249 123.778 2122 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.34 % Allowed : 17.56 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.20), residues: 1825 helix: -0.21 (0.21), residues: 664 sheet: -1.19 (0.28), residues: 361 loop : -0.93 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.009 0.001 TYR C 166 PHE 0.008 0.001 PHE B 262 TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (14969) covalent geometry : angle 0.62264 / 0.30 (20319) hydrogen bonds : bond 0.02847 / 1.96 ( 511) hydrogen bonds : angle 4.83800 / 3.43 ( 1350) Misc. bond : bond 0.00036 / 0.02 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1947.67 seconds wall clock time: 34 minutes 45.53 seconds (2085.53 seconds total)