Starting phenix.real_space_refine on Thu Mar 5 05:23:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q8s_13865/03_2026/7q8s_13865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q8s_13865/03_2026/7q8s_13865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q8s_13865/03_2026/7q8s_13865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q8s_13865/03_2026/7q8s_13865.map" model { file = "/net/cci-nas-00/data/ceres_data/7q8s_13865/03_2026/7q8s_13865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q8s_13865/03_2026/7q8s_13865.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 135 5.16 5 C 12355 2.51 5 N 3350 2.21 5 O 3810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19665 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2815 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 21, 'TRANS': 337} Chain breaks: 1 Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1090 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} 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} Restraints were copied for chains: C, D, E, F, G, H, I, J Time building chain proxies: 3.18, per 1000 atoms: 0.16 Number of scatterers: 19665 At special positions: 0 Unit cell: (103.404, 114.606, 205.946, 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 135 16.00 P 10 15.00 Mg 5 11.99 O 3810 8.00 N 3350 7.00 C 12355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 930.7 milliseconds 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 35 sheets defined 49.5% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.679A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 4.144A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.520A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 175 removed outlier: 4.221A pdb=" N VAL A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.510A pdb=" N LEU A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 214 removed outlier: 3.627A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.841A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.569A pdb=" N ARG A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 256' Processing helix chain 'A' and resid 257 through 262 removed outlier: 4.340A pdb=" N PHE A 261 " --> pdb=" O PRO A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.630A pdb=" N ILE A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 284 through 285 No H-bonds generated for 'chain 'A' and resid 284 through 285' Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.886A pdb=" N GLY A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.538A pdb=" N LYS A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.911A pdb=" N GLN A 353 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.596A pdb=" N ASN A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 21 removed outlier: 4.119A pdb=" N ARG B 13 " --> pdb=" O GLU B 9 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 55 removed outlier: 3.653A pdb=" N LEU B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 55 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.674A pdb=" N SER B 108 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.860A pdb=" N HIS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.679A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 4.144A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 100 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.521A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 175 removed outlier: 4.221A pdb=" N VAL C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.510A pdb=" N LEU C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.626A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 234 removed outlier: 3.841A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.568A pdb=" N ARG C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 256' Processing helix chain 'C' and resid 257 through 262 removed outlier: 4.339A pdb=" N PHE C 261 " --> pdb=" O PRO C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.630A pdb=" N ILE C 266 " --> pdb=" O PRO C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 284 through 285 No H-bonds generated for 'chain 'C' and resid 284 through 285' Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.886A pdb=" N GLY C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.538A pdb=" N LYS C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.911A pdb=" N GLN C 353 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.596A pdb=" N ASN C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 21 removed outlier: 4.119A pdb=" N ARG G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 55 removed outlier: 3.653A pdb=" N LEU G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 55 " --> pdb=" O THR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 102 Processing helix chain 'G' and resid 103 through 109 removed outlier: 3.674A pdb=" N SER G 108 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 125 through 136 removed outlier: 3.859A pdb=" N HIS G 136 " --> pdb=" O LYS G 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.679A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 4.144A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 100 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.521A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 175 removed outlier: 4.221A pdb=" N VAL D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.510A pdb=" N LEU D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 214 removed outlier: 3.626A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.841A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.569A pdb=" N ARG D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS D 256 " --> pdb=" O GLN D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 256' Processing helix chain 'D' and resid 257 through 262 removed outlier: 4.339A pdb=" N PHE D 261 " --> pdb=" O PRO D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.630A pdb=" N ILE D 266 " --> pdb=" O PRO D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.886A pdb=" N GLY D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.538A pdb=" N LYS D 315 " --> pdb=" O GLU D 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.910A pdb=" N GLN D 353 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.596A pdb=" N ASN D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 21 removed outlier: 4.119A pdb=" N ARG H 13 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 55 removed outlier: 3.653A pdb=" N LEU H 53 " --> pdb=" O ASN H 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU H 55 " --> pdb=" O THR H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 103 through 109 removed outlier: 3.674A pdb=" N SER H 108 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 125 through 136 removed outlier: 3.860A pdb=" N HIS H 136 " --> pdb=" O LYS H 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.678A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 removed outlier: 4.143A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 100 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.521A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 175 removed outlier: 4.221A pdb=" N VAL E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.510A pdb=" N LEU E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 214 removed outlier: 3.626A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 234 removed outlier: 3.841A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 256 removed outlier: 3.569A pdb=" N ARG E 255 " --> pdb=" O ASN E 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 251 through 256' Processing helix chain 'E' and resid 257 through 262 removed outlier: 4.339A pdb=" N PHE E 261 " --> pdb=" O PRO E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 removed outlier: 3.630A pdb=" N ILE E 266 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 284 through 285 No H-bonds generated for 'chain 'E' and resid 284 through 285' Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.886A pdb=" N GLY E 295 " --> pdb=" O ARG E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.539A pdb=" N LYS E 315 " --> pdb=" O GLU E 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 349 through 355 removed outlier: 3.910A pdb=" N GLN E 353 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.596A pdb=" N ASN E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 21 removed outlier: 4.119A pdb=" N ARG I 13 " --> pdb=" O GLU I 9 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY I 14 " --> pdb=" O GLU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 55 removed outlier: 3.653A pdb=" N LEU I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 109 removed outlier: 3.674A pdb=" N SER I 108 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 125 through 136 removed outlier: 3.859A pdb=" N HIS I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.679A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 92 removed outlier: 4.143A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 100 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.520A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET F 123 " --> pdb=" O MET F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 172 through 175 removed outlier: 4.221A pdb=" N VAL F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 193 removed outlier: 3.510A pdb=" N LEU F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 214 removed outlier: 3.627A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 234 removed outlier: 3.841A pdb=" N ALA F 231 " --> pdb=" O MET F 227 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS F 232 " --> pdb=" O THR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 256 removed outlier: 3.569A pdb=" N ARG F 255 " --> pdb=" O ASN F 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS F 256 " --> pdb=" O GLN F 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 251 through 256' Processing helix chain 'F' and resid 257 through 262 removed outlier: 4.339A pdb=" N PHE F 261 " --> pdb=" O PRO F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.630A pdb=" N ILE F 266 " --> pdb=" O PRO F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.886A pdb=" N GLY F 295 " --> pdb=" O ARG F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.539A pdb=" N LYS F 315 " --> pdb=" O GLU F 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 349 through 355 removed outlier: 3.910A pdb=" N GLN F 353 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.596A pdb=" N ASN F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 21 removed outlier: 4.118A pdb=" N ARG J 13 " --> pdb=" O GLU J 9 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY J 14 " --> pdb=" O GLU J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 55 removed outlier: 3.653A pdb=" N LEU J 53 " --> pdb=" O ASN J 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 103 through 109 removed outlier: 3.674A pdb=" N SER J 108 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 124 Processing helix chain 'J' and resid 125 through 136 removed outlier: 3.859A pdb=" N HIS J 136 " --> pdb=" O LYS J 132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.982A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLY A 135 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 105 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.921A pdb=" N GLU A 72 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.725A pdb=" N THR A 162 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 176 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.461A pdb=" N ILE A 297 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 240 Processing sheet with id=AA7, first strand: chain 'B' and resid 7 through 8 removed outlier: 7.175A pdb=" N THR B 7 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N VAL B 40 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET B 28 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 43 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR B 26 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU B 114 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 81 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE B 116 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 83 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA B 118 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN B 85 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.982A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLY C 135 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU C 105 " --> pdb=" O GLY C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.921A pdb=" N GLU C 72 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.726A pdb=" N THR C 162 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG C 176 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.461A pdb=" N ILE C 297 " --> pdb=" O VAL C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=AB5, first strand: chain 'G' and resid 7 through 8 removed outlier: 7.175A pdb=" N THR G 7 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N VAL G 40 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET G 28 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL G 43 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR G 26 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU G 114 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU G 81 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE G 116 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU G 83 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA G 118 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN G 85 " --> pdb=" O ALA G 118 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.982A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY D 135 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU D 105 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB8, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.921A pdb=" N GLU D 72 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.725A pdb=" N THR D 162 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D 176 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.461A pdb=" N ILE D 297 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 237 through 240 Processing sheet with id=AC3, first strand: chain 'H' and resid 7 through 8 removed outlier: 7.175A pdb=" N THR H 7 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N VAL H 40 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET H 28 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL H 43 " --> pdb=" O TYR H 26 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N LEU H 114 " --> pdb=" O GLU H 79 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU H 81 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE H 116 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU H 83 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA H 118 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN H 85 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.982A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY E 135 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU E 105 " --> pdb=" O GLY E 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'E' and resid 71 through 72 removed outlier: 3.921A pdb=" N GLU E 72 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE E 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.725A pdb=" N THR E 162 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG E 176 " --> pdb=" O THR E 162 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.461A pdb=" N ILE E 297 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 237 through 240 Processing sheet with id=AD1, first strand: chain 'I' and resid 7 through 8 removed outlier: 7.176A pdb=" N THR I 7 " --> pdb=" O ILE I 38 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N VAL I 40 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET I 28 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL I 43 " --> pdb=" O TYR I 26 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR I 26 " --> pdb=" O VAL I 43 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU I 114 " --> pdb=" O GLU I 79 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU I 81 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE I 116 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU I 83 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA I 118 " --> pdb=" O LEU I 83 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN I 85 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.982A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLY F 135 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU F 105 " --> pdb=" O GLY F 135 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'F' and resid 71 through 72 removed outlier: 3.921A pdb=" N GLU F 72 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE F 75 " --> pdb=" O GLU F 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.725A pdb=" N THR F 162 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG F 176 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.461A pdb=" N ILE F 297 " --> pdb=" O VAL F 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 237 through 240 Processing sheet with id=AD8, first strand: chain 'J' and resid 7 through 8 removed outlier: 7.176A pdb=" N THR J 7 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N VAL J 40 " --> pdb=" O THR J 7 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET J 28 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL J 43 " --> pdb=" O TYR J 26 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR J 26 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N LEU J 114 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU J 81 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE J 116 " --> pdb=" O LEU J 81 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU J 83 " --> pdb=" O ILE J 116 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA J 118 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN J 85 " --> pdb=" O ALA J 118 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2100 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: 3.72 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6468 1.34 - 1.46: 4007 1.46 - 1.58: 9325 1.58 - 1.69: 15 1.69 - 1.81: 235 Bond restraints: 20050 Sorted by residual: bond pdb=" C4 ADP C 600 " pdb=" C5 ADP C 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C4 ADP F 600 " pdb=" C5 ADP F 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" C4 ADP A 600 " pdb=" C5 ADP A 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.07e+00 ... (remaining 20045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 26663 1.20 - 2.40: 251 2.40 - 3.60: 131 3.60 - 4.80: 35 4.80 - 6.01: 30 Bond angle restraints: 27110 Sorted by residual: angle pdb=" O1B ADP C 600 " pdb=" PB ADP C 600 " pdb=" O2B ADP C 600 " ideal model delta sigma weight residual 119.90 113.89 6.01 3.00e+00 1.11e-01 4.01e+00 angle pdb=" O1B ADP D 600 " pdb=" PB ADP D 600 " pdb=" O2B ADP D 600 " ideal model delta sigma weight residual 119.90 113.92 5.98 3.00e+00 1.11e-01 3.98e+00 angle pdb=" O1B ADP E 600 " pdb=" PB ADP E 600 " pdb=" O2B ADP E 600 " ideal model delta sigma weight residual 119.90 113.93 5.97 3.00e+00 1.11e-01 3.95e+00 angle pdb=" O1B ADP F 600 " pdb=" PB ADP F 600 " pdb=" O2B ADP F 600 " ideal model delta sigma weight residual 119.90 113.94 5.96 3.00e+00 1.11e-01 3.95e+00 angle pdb=" O1B ADP A 600 " pdb=" PB ADP A 600 " pdb=" O2B ADP A 600 " ideal model delta sigma weight residual 119.90 113.98 5.92 3.00e+00 1.11e-01 3.89e+00 ... (remaining 27105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.26: 12061 23.26 - 46.51: 144 46.51 - 69.77: 15 69.77 - 93.02: 5 93.02 - 116.28: 5 Dihedral angle restraints: 12230 sinusoidal: 5045 harmonic: 7185 Sorted by residual: dihedral pdb=" O1B ADP C 600 " pdb=" O3A ADP C 600 " pdb=" PB ADP C 600 " pdb=" PA ADP C 600 " ideal model delta sinusoidal sigma weight residual -60.00 -176.28 116.28 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" O1B ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PB ADP F 600 " pdb=" PA ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -176.28 116.28 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 -176.27 116.26 1 2.00e+01 2.50e-03 3.46e+01 ... (remaining 12227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1599 0.025 - 0.051: 778 0.051 - 0.076: 313 0.076 - 0.101: 183 0.101 - 0.126: 122 Chirality restraints: 2995 Sorted by residual: chirality pdb=" CA ILE H 38 " pdb=" N ILE H 38 " pdb=" C ILE H 38 " pdb=" CB ILE H 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE I 38 " pdb=" N ILE I 38 " pdb=" C ILE I 38 " pdb=" CB ILE I 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE J 38 " pdb=" N ILE J 38 " pdb=" C ILE J 38 " pdb=" CB ILE J 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 2992 not shown) Planarity restraints: 3485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 108 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO C 109 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 108 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO D 109 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 109 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 109 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 108 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO A 109 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.015 5.00e-02 4.00e+02 ... (remaining 3482 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2760 2.76 - 3.29: 17987 3.29 - 3.83: 29193 3.83 - 4.36: 36266 4.36 - 4.90: 64675 Nonbonded interactions: 150881 Sorted by model distance: nonbonded pdb=" OD1 ASP G 120 " pdb=" OG SER G 122 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP H 120 " pdb=" OG SER H 122 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP J 120 " pdb=" OG SER J 122 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP B 120 " pdb=" OG SER B 122 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP I 120 " pdb=" OG SER I 122 " model vdw 2.223 3.040 ... (remaining 150876 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.002 0.021 20050 Z= 0.075 Angle : 0.442 6.006 27110 Z= 0.212 Chirality : 0.043 0.126 2995 Planarity : 0.003 0.027 3485 Dihedral : 8.150 116.277 7610 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.23 % Allowed : 1.38 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.17), residues: 2455 helix: 0.75 (0.18), residues: 805 sheet: 1.28 (0.22), residues: 520 loop : 0.97 (0.20), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 103 TYR 0.006 0.001 TYR B 71 PHE 0.005 0.001 PHE D 254 TRP 0.003 0.001 TRP F 86 HIS 0.002 0.000 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00157 (20050) covalent geometry : angle 0.44239 (27110) hydrogen bonds : bond 0.27790 ( 800) hydrogen bonds : angle 6.93243 ( 2100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 355 time to evaluate : 0.760 Fit side-chains REVERT: A 82 MET cc_start: 0.9145 (tpt) cc_final: 0.8820 (tpt) REVERT: A 193 MET cc_start: 0.8517 (tpp) cc_final: 0.8228 (tpt) REVERT: B 120 ASP cc_start: 0.7807 (p0) cc_final: 0.7577 (p0) REVERT: C 193 MET cc_start: 0.8628 (tpp) cc_final: 0.8289 (tpt) REVERT: C 247 MET cc_start: 0.7697 (ttp) cc_final: 0.7453 (ttm) REVERT: G 120 ASP cc_start: 0.7855 (p0) cc_final: 0.7558 (p0) REVERT: E 82 MET cc_start: 0.9028 (tpt) cc_final: 0.8605 (tpt) REVERT: I 125 ASP cc_start: 0.7800 (t0) cc_final: 0.6793 (t70) REVERT: F 82 MET cc_start: 0.9233 (tpt) cc_final: 0.8763 (tpt) REVERT: F 248 MET cc_start: 0.8724 (mmt) cc_final: 0.8364 (mmt) outliers start: 5 outliers final: 3 residues processed: 360 average time/residue: 0.1811 time to fit residues: 93.5225 Evaluate side-chains 210 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain I residue 27 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.0970 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 0.0060 overall best weight: 0.8356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 85 GLN G 85 GLN H 85 GLN I 85 GLN F 215 GLN J 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.088171 restraints weight = 34666.578| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.70 r_work: 0.2962 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20050 Z= 0.102 Angle : 0.536 6.635 27110 Z= 0.265 Chirality : 0.045 0.166 2995 Planarity : 0.004 0.043 3485 Dihedral : 6.550 103.189 2758 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.38 % Allowed : 3.92 % Favored : 94.70 % 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: 1.42 (0.18), residues: 2455 helix: 1.22 (0.18), residues: 895 sheet: 1.00 (0.22), residues: 525 loop : 0.86 (0.21), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 92 TYR 0.009 0.001 TYR H 71 PHE 0.007 0.001 PHE F 31 TRP 0.006 0.001 TRP E 86 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00206 (20050) covalent geometry : angle 0.53601 (27110) hydrogen bonds : bond 0.04214 ( 800) hydrogen bonds : angle 4.80234 ( 2100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.601 Fit side-chains REVERT: A 187 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: A 226 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7736 (mm-30) REVERT: C 187 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: C 193 MET cc_start: 0.9179 (tpp) cc_final: 0.8851 (tpt) REVERT: G 120 ASP cc_start: 0.8327 (p0) cc_final: 0.8105 (p0) REVERT: D 187 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: E 187 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: I 18 ASP cc_start: 0.8003 (m-30) cc_final: 0.7799 (m-30) REVERT: F 187 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: J 42 GLU cc_start: 0.8080 (tt0) cc_final: 0.7876 (tm-30) outliers start: 30 outliers final: 13 residues processed: 266 average time/residue: 0.1330 time to fit residues: 55.6477 Evaluate side-chains 229 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 0.0670 chunk 126 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 75 optimal weight: 0.0980 overall best weight: 0.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN J 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.089241 restraints weight = 34847.008| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.66 r_work: 0.2967 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 20050 Z= 0.084 Angle : 0.488 6.760 27110 Z= 0.235 Chirality : 0.044 0.123 2995 Planarity : 0.003 0.030 3485 Dihedral : 6.258 96.510 2758 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.88 % Allowed : 4.93 % Favored : 94.19 % 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: 1.55 (0.18), residues: 2455 helix: 1.54 (0.18), residues: 925 sheet: 0.78 (0.22), residues: 525 loop : 0.88 (0.22), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 131 TYR 0.008 0.001 TYR H 71 PHE 0.006 0.001 PHE H 67 TRP 0.002 0.000 TRP E 340 HIS 0.003 0.000 HIS J 136 Details of bonding type rmsd covalent geometry : bond 0.00171 (20050) covalent geometry : angle 0.48829 (27110) hydrogen bonds : bond 0.03537 ( 800) hydrogen bonds : angle 4.33783 ( 2100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.758 Fit side-chains REVERT: A 240 GLU cc_start: 0.8511 (tt0) cc_final: 0.8231 (mp0) REVERT: B 92 ARG cc_start: 0.8084 (mmp80) cc_final: 0.7843 (mmp-170) REVERT: B 120 ASP cc_start: 0.8145 (p0) cc_final: 0.7937 (p0) REVERT: C 193 MET cc_start: 0.9199 (tpp) cc_final: 0.8871 (tpt) REVERT: C 226 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7670 (mm-30) REVERT: G 120 ASP cc_start: 0.8308 (p0) cc_final: 0.8070 (p0) REVERT: I 18 ASP cc_start: 0.8067 (m-30) cc_final: 0.7817 (m-30) REVERT: J 42 GLU cc_start: 0.8156 (tt0) cc_final: 0.7936 (tm-30) outliers start: 19 outliers final: 15 residues processed: 243 average time/residue: 0.1197 time to fit residues: 46.3722 Evaluate side-chains 224 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 177 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 193 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 196 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN G 85 GLN D 121 GLN D 215 GLN H 85 GLN I 85 GLN J 85 GLN J 136 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.081860 restraints weight = 35195.386| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.68 r_work: 0.2831 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 20050 Z= 0.282 Angle : 0.660 7.342 27110 Z= 0.332 Chirality : 0.052 0.151 2995 Planarity : 0.005 0.048 3485 Dihedral : 7.539 116.535 2758 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.71 % Allowed : 5.39 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2455 helix: 1.27 (0.17), residues: 895 sheet: 0.52 (0.22), residues: 520 loop : 0.28 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 137 TYR 0.027 0.002 TYR H 71 PHE 0.014 0.002 PHE G 69 TRP 0.014 0.002 TRP A 79 HIS 0.007 0.002 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00702 (20050) covalent geometry : angle 0.65995 (27110) hydrogen bonds : bond 0.05535 ( 800) hydrogen bonds : angle 4.66232 ( 2100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.663 Fit side-chains REVERT: A 187 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 270 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7379 (pm20) REVERT: B 120 ASP cc_start: 0.8430 (p0) cc_final: 0.8201 (p0) REVERT: C 187 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: C 193 MET cc_start: 0.9210 (tpp) cc_final: 0.8907 (tpt) REVERT: C 226 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7932 (mm-30) REVERT: G 120 ASP cc_start: 0.8510 (p0) cc_final: 0.8255 (p0) REVERT: D 187 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: E 187 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: I 18 ASP cc_start: 0.8115 (m-30) cc_final: 0.7774 (m-30) REVERT: F 187 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: J 42 GLU cc_start: 0.8150 (tt0) cc_final: 0.7940 (tt0) outliers start: 37 outliers final: 28 residues processed: 244 average time/residue: 0.1279 time to fit residues: 49.8187 Evaluate side-chains 236 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 175 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN J 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.084772 restraints weight = 34729.108| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.63 r_work: 0.2887 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20050 Z= 0.111 Angle : 0.520 6.591 27110 Z= 0.255 Chirality : 0.046 0.124 2995 Planarity : 0.004 0.035 3485 Dihedral : 6.994 110.760 2758 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.38 % Allowed : 6.73 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.18), residues: 2455 helix: 1.52 (0.18), residues: 865 sheet: 0.41 (0.22), residues: 525 loop : 0.44 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.012 0.001 TYR I 71 PHE 0.008 0.001 PHE A 31 TRP 0.005 0.001 TRP A 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00262 (20050) covalent geometry : angle 0.51968 (27110) hydrogen bonds : bond 0.03662 ( 800) hydrogen bonds : angle 4.33445 ( 2100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.825 Fit side-chains REVERT: A 187 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: B 92 ARG cc_start: 0.8198 (mmp80) cc_final: 0.7956 (mmt-90) REVERT: C 187 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: C 193 MET cc_start: 0.9187 (tpp) cc_final: 0.8880 (tpt) REVERT: C 226 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7788 (mm-30) REVERT: G 120 ASP cc_start: 0.8474 (p0) cc_final: 0.8227 (p0) REVERT: D 154 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7810 (t70) REVERT: D 187 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: E 187 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: I 18 ASP cc_start: 0.8070 (m-30) cc_final: 0.7742 (m-30) REVERT: F 187 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: J 42 GLU cc_start: 0.8134 (tt0) cc_final: 0.7912 (tt0) outliers start: 30 outliers final: 20 residues processed: 234 average time/residue: 0.1402 time to fit residues: 51.9140 Evaluate side-chains 230 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 27 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 38 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN E 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.099401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.081820 restraints weight = 35008.830| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.65 r_work: 0.2834 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 20050 Z= 0.224 Angle : 0.608 6.691 27110 Z= 0.304 Chirality : 0.049 0.142 2995 Planarity : 0.005 0.040 3485 Dihedral : 7.592 117.666 2758 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.98 % Allowed : 6.68 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2455 helix: 1.41 (0.18), residues: 835 sheet: 0.34 (0.22), residues: 520 loop : 0.21 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 137 TYR 0.020 0.002 TYR I 71 PHE 0.013 0.002 PHE J 69 TRP 0.010 0.002 TRP E 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00560 (20050) covalent geometry : angle 0.60781 (27110) hydrogen bonds : bond 0.04844 ( 800) hydrogen bonds : angle 4.50873 ( 2100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.843 Fit side-chains REVERT: A 187 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: B 92 ARG cc_start: 0.8261 (mmp80) cc_final: 0.7997 (mmt-90) REVERT: C 187 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: C 193 MET cc_start: 0.9163 (tpp) cc_final: 0.8890 (tpt) REVERT: C 226 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7717 (mm-30) REVERT: G 120 ASP cc_start: 0.8585 (p0) cc_final: 0.8311 (p0) REVERT: D 154 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7793 (t70) REVERT: D 187 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: E 187 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: I 18 ASP cc_start: 0.8104 (m-30) cc_final: 0.7750 (m-30) REVERT: F 187 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: J 42 GLU cc_start: 0.8103 (tt0) cc_final: 0.7856 (tt0) outliers start: 43 outliers final: 29 residues processed: 248 average time/residue: 0.1262 time to fit residues: 50.4188 Evaluate side-chains 241 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 66 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.081232 restraints weight = 35051.333| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.78 r_work: 0.2829 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20050 Z= 0.189 Angle : 0.579 6.794 27110 Z= 0.289 Chirality : 0.048 0.140 2995 Planarity : 0.004 0.037 3485 Dihedral : 7.483 117.404 2758 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.21 % Allowed : 7.47 % Favored : 90.32 % 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: 0.82 (0.17), residues: 2455 helix: 1.38 (0.19), residues: 835 sheet: -0.01 (0.21), residues: 560 loop : 0.35 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.015 0.001 TYR H 71 PHE 0.010 0.002 PHE D 31 TRP 0.007 0.001 TRP A 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00473 (20050) covalent geometry : angle 0.57889 (27110) hydrogen bonds : bond 0.04349 ( 800) hydrogen bonds : angle 4.44818 ( 2100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.738 Fit side-chains REVERT: A 187 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: B 92 ARG cc_start: 0.8238 (mmp80) cc_final: 0.7975 (mmt-90) REVERT: C 187 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: C 193 MET cc_start: 0.9153 (tpp) cc_final: 0.8851 (tpt) REVERT: C 226 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7650 (mm-30) REVERT: G 120 ASP cc_start: 0.8597 (p0) cc_final: 0.8299 (p0) REVERT: D 154 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7921 (t70) REVERT: D 187 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: E 187 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: I 18 ASP cc_start: 0.8078 (m-30) cc_final: 0.7739 (m-30) REVERT: F 187 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: J 42 GLU cc_start: 0.8172 (tt0) cc_final: 0.7910 (tt0) outliers start: 48 outliers final: 37 residues processed: 252 average time/residue: 0.1190 time to fit residues: 49.0247 Evaluate side-chains 247 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 203 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.083312 restraints weight = 34773.356| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.63 r_work: 0.2860 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20050 Z= 0.133 Angle : 0.544 6.657 27110 Z= 0.267 Chirality : 0.046 0.127 2995 Planarity : 0.004 0.035 3485 Dihedral : 7.181 113.397 2758 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.71 % Allowed : 8.43 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2455 helix: 1.50 (0.19), residues: 835 sheet: 0.11 (0.22), residues: 535 loop : 0.41 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.012 0.001 TYR H 71 PHE 0.009 0.001 PHE A 31 TRP 0.006 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00324 (20050) covalent geometry : angle 0.54366 (27110) hydrogen bonds : bond 0.03739 ( 800) hydrogen bonds : angle 4.30341 ( 2100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.831 Fit side-chains REVERT: A 187 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: B 92 ARG cc_start: 0.8160 (mmp80) cc_final: 0.7911 (mmt-90) REVERT: C 187 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: C 193 MET cc_start: 0.9148 (tpp) cc_final: 0.8835 (tpt) REVERT: C 226 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7723 (mm-30) REVERT: G 120 ASP cc_start: 0.8552 (p0) cc_final: 0.8266 (p0) REVERT: D 154 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7963 (t70) REVERT: D 187 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: E 187 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: I 18 ASP cc_start: 0.8071 (m-30) cc_final: 0.7761 (m-30) REVERT: F 187 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: J 42 GLU cc_start: 0.8159 (tt0) cc_final: 0.7899 (tt0) outliers start: 37 outliers final: 29 residues processed: 236 average time/residue: 0.1296 time to fit residues: 49.7434 Evaluate side-chains 235 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 204 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.101380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.082565 restraints weight = 34461.542| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.81 r_work: 0.2869 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20050 Z= 0.109 Angle : 0.521 6.619 27110 Z= 0.254 Chirality : 0.045 0.125 2995 Planarity : 0.004 0.034 3485 Dihedral : 6.884 107.967 2758 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.80 % Allowed : 8.39 % Favored : 89.82 % 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: 1.12 (0.18), residues: 2455 helix: 1.63 (0.19), residues: 835 sheet: 0.14 (0.22), residues: 535 loop : 0.52 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.010 0.001 TYR J 71 PHE 0.008 0.001 PHE A 31 TRP 0.005 0.001 TRP D 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00260 (20050) covalent geometry : angle 0.52121 (27110) hydrogen bonds : bond 0.03342 ( 800) hydrogen bonds : angle 4.17736 ( 2100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.743 Fit side-chains REVERT: A 187 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: A 240 GLU cc_start: 0.8591 (tt0) cc_final: 0.8281 (mp0) REVERT: B 92 ARG cc_start: 0.8100 (mmp80) cc_final: 0.7847 (mmt-90) REVERT: C 187 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: C 193 MET cc_start: 0.9141 (tpp) cc_final: 0.8896 (tpt) REVERT: G 120 ASP cc_start: 0.8509 (p0) cc_final: 0.8156 (p0) REVERT: D 154 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8007 (t70) REVERT: D 187 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: E 187 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: I 18 ASP cc_start: 0.7982 (m-30) cc_final: 0.7688 (m-30) REVERT: F 187 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: J 42 GLU cc_start: 0.8221 (tt0) cc_final: 0.7975 (tt0) outliers start: 39 outliers final: 28 residues processed: 235 average time/residue: 0.1272 time to fit residues: 48.5995 Evaluate side-chains 233 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 140 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 239 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.084868 restraints weight = 34892.942| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.66 r_work: 0.2898 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20050 Z= 0.091 Angle : 0.510 7.612 27110 Z= 0.246 Chirality : 0.044 0.125 2995 Planarity : 0.003 0.033 3485 Dihedral : 6.597 102.906 2758 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.47 % Allowed : 8.94 % Favored : 89.59 % 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: 1.23 (0.18), residues: 2455 helix: 1.74 (0.19), residues: 835 sheet: 0.14 (0.22), residues: 535 loop : 0.61 (0.21), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.008 0.001 TYR J 71 PHE 0.007 0.001 PHE A 31 TRP 0.004 0.001 TRP F 340 HIS 0.002 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00208 (20050) covalent geometry : angle 0.50953 (27110) hydrogen bonds : bond 0.03023 ( 800) hydrogen bonds : angle 4.08834 ( 2100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.806 Fit side-chains REVERT: A 187 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 240 GLU cc_start: 0.8540 (tt0) cc_final: 0.8307 (mp0) REVERT: B 92 ARG cc_start: 0.8119 (mmp80) cc_final: 0.7893 (mmt-90) REVERT: C 187 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: C 193 MET cc_start: 0.9154 (tpp) cc_final: 0.8881 (tpt) REVERT: G 120 ASP cc_start: 0.8466 (p0) cc_final: 0.8172 (p0) REVERT: D 187 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: E 187 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: I 18 ASP cc_start: 0.8031 (m-30) cc_final: 0.7753 (m-30) REVERT: F 187 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: J 42 GLU cc_start: 0.8178 (tt0) cc_final: 0.7968 (tt0) outliers start: 32 outliers final: 26 residues processed: 227 average time/residue: 0.1271 time to fit residues: 47.0359 Evaluate side-chains 229 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 7.9990 chunk 85 optimal weight: 0.0370 chunk 7 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 chunk 127 optimal weight: 0.0970 chunk 87 optimal weight: 9.9990 overall best weight: 1.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.085107 restraints weight = 34866.642| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.66 r_work: 0.2904 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20050 Z= 0.092 Angle : 0.508 6.879 27110 Z= 0.245 Chirality : 0.044 0.125 2995 Planarity : 0.003 0.032 3485 Dihedral : 6.419 98.318 2758 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.80 % Allowed : 8.66 % Favored : 89.54 % 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: 1.26 (0.18), residues: 2455 helix: 1.76 (0.19), residues: 845 sheet: 0.13 (0.22), residues: 535 loop : 0.63 (0.21), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.009 0.001 TYR B 71 PHE 0.007 0.001 PHE A 31 TRP 0.004 0.001 TRP F 79 HIS 0.003 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00211 (20050) covalent geometry : angle 0.50793 (27110) hydrogen bonds : bond 0.03011 ( 800) hydrogen bonds : angle 4.04782 ( 2100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4129.99 seconds wall clock time: 71 minutes 41.41 seconds (4301.41 seconds total)