Starting phenix.real_space_refine on Sun Aug 24 15:22:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f8r_28934/08_2025/8f8r_28934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8r_28934/08_2025/8f8r_28934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f8r_28934/08_2025/8f8r_28934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8r_28934/08_2025/8f8r_28934.map" model { file = "/net/cci-nas-00/data/ceres_data/8f8r_28934/08_2025/8f8r_28934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8r_28934/08_2025/8f8r_28934.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 14 5.49 5 Mg 7 5.21 5 S 147 5.16 5 C 12941 2.51 5 N 3462 2.21 5 O 3955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20526 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.01, per 1000 atoms: 0.20 Number of scatterers: 20526 At special positions: 0 Unit cell: (86.4, 108, 250.56, 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 147 16.00 P 14 15.00 Mg 7 11.99 O 3955 8.00 N 3462 7.00 C 12941 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: 1.71 Conformation dependent library (CDL) restraints added in 648.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4810 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 42 sheets defined 49.6% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.656A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.641A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.812A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.555A pdb=" N ILE 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 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.725A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.616A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.579A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.569A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 321 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 347 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.963A pdb=" N GLN 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 367 through 372 removed outlier: 5.343A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.768A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.683A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.825A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.701A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.523A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.616A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.551A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.518A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.664A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 305' Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.162A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.955A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.541A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.720A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.913A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.718A pdb=" N ILE 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 194 removed outlier: 3.729A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.901A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.751A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.691A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.567A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (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 347 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.128A pdb=" N GLN 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 374 removed outlier: 4.090A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.530A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.589A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.838A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.796A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.659A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.521A pdb=" N PHE D 266 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 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: 3.528A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.525A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 301 through 305' Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.505A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (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 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.108A pdb=" N GLN 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 374 removed outlier: 3.998A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.548A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.560A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.950A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.643A pdb=" N ILE 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 Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.769A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.759A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 removed outlier: 3.575A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.603A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (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 Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.578A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.520A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (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 347 Processing helix chain 'E' and resid 351 through 355 removed outlier: 4.198A pdb=" N GLN 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: 4.289A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.636A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.639A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.821A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 205 through 217 removed outlier: 3.670A pdb=" N CYS F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.672A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.508A pdb=" N LEU F 293 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA F 295 " --> pdb=" O LYS 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: 3.562A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (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 347 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.657A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.606A pdb=" N GLU G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 101' Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.904A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.739A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.646A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 removed outlier: 3.525A pdb=" N ILE G 267 " --> pdb=" O PRO G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 284 removed outlier: 3.506A pdb=" N LYS G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 296 removed outlier: 3.515A pdb=" N ALA G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 removed outlier: 3.776A pdb=" N MET G 305 " --> pdb=" O GLY G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 removed outlier: 3.573A pdb=" N ARG G 312 " --> pdb=" O GLY G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 347 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.302A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 105 " --> pdb=" O ALA 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.353A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.123A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.522A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.315A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.257A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.438A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 5.989A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.014A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.451A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.027A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 4.094A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.593A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 176 through 178 removed outlier: 5.976A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 176 through 178 removed outlier: 4.203A pdb=" N GLN G 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.510A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.110A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.381A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.598A pdb=" N ASN G 162 " --> pdb=" O MET G 176 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET G 176 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.162A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 238 through 241 928 hydrogen bonds defined for protein. 2412 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: 3.48 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6618 1.34 - 1.46: 4627 1.46 - 1.58: 9447 1.58 - 1.70: 21 1.70 - 1.82: 259 Bond restraints: 20972 Sorted by residual: bond pdb=" C LEU G 242 " pdb=" N PRO G 243 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.08e-02 8.57e+03 8.02e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.67e+00 ... (remaining 20967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 27987 3.19 - 6.37: 416 6.37 - 9.56: 47 9.56 - 12.75: 9 12.75 - 15.94: 4 Bond angle restraints: 28463 Sorted by residual: angle pdb=" CA MET D 47 " pdb=" CB MET D 47 " pdb=" CG MET D 47 " ideal model delta sigma weight residual 114.10 124.83 -10.73 2.00e+00 2.50e-01 2.88e+01 angle pdb=" CA MET C 47 " pdb=" CB MET C 47 " pdb=" CG MET C 47 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.83e+01 angle pdb=" CB MET F 44 " pdb=" CG MET F 44 " pdb=" SD MET F 44 " ideal model delta sigma weight residual 112.70 128.64 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" C ILE E 282 " pdb=" N MET E 283 " pdb=" CA MET E 283 " ideal model delta sigma weight residual 122.66 114.52 8.14 1.63e+00 3.76e-01 2.49e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 ... (remaining 28458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 12362 33.69 - 67.38: 204 67.38 - 101.08: 37 101.08 - 134.77: 7 134.77 - 168.46: 7 Dihedral angle restraints: 12617 sinusoidal: 5101 harmonic: 7516 Sorted by residual: dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.46 -168.46 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 104.91 -164.91 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.58 -163.57 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 12614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2347 0.057 - 0.113: 655 0.113 - 0.170: 134 0.170 - 0.227: 20 0.227 - 0.283: 5 Chirality restraints: 3161 Sorted by residual: chirality pdb=" CB ILE F 151 " pdb=" CA ILE F 151 " pdb=" CG1 ILE F 151 " pdb=" CG2 ILE F 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA MET D 47 " pdb=" N MET D 47 " pdb=" C MET D 47 " pdb=" CB MET D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA MET F 47 " pdb=" N MET F 47 " pdb=" C MET F 47 " pdb=" CB MET F 47 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3158 not shown) Planarity restraints: 3639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 37 " -0.056 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO F 38 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO F 38 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 38 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 37 " -0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 38 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 37 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.17e+01 pdb=" N PRO A 38 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.046 5.00e-02 4.00e+02 ... (remaining 3636 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 177 2.61 - 3.19: 16189 3.19 - 3.76: 31283 3.76 - 4.33: 44493 4.33 - 4.90: 73733 Nonbonded interactions: 165875 Sorted by model distance: nonbonded pdb=" O1B ADP G 401 " pdb="MG MG G 402 " model vdw 2.042 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.085 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.114 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.138 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.172 2.170 ... (remaining 165870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'B' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'F' and resid 5 through 402) selection = chain 'G' } 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: 5.990 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: 0.040 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.560 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.005 0.062 20972 Z= 0.235 Angle : 0.962 15.935 28463 Z= 0.512 Chirality : 0.055 0.283 3161 Planarity : 0.010 0.089 3639 Dihedral : 15.053 168.459 7807 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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 aren not related in a simple way. whole: -1.91 (0.15), residues: 2566 helix: -2.16 (0.12), residues: 1083 sheet: -0.23 (0.24), residues: 456 loop : -0.41 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 210 TYR 0.031 0.002 TYR E 279 PHE 0.039 0.002 PHE F 127 TRP 0.019 0.002 TRP A 356 HIS 0.018 0.001 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00491 (20972) covalent geometry : angle 0.96157 (28463) hydrogen bonds : bond 0.16298 ( 904) hydrogen bonds : angle 6.98305 ( 2412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.9423 (tpp) cc_final: 0.9201 (tpt) REVERT: B 361 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8986 (mp0) REVERT: B 372 ARG cc_start: 0.8548 (ptp90) cc_final: 0.8168 (ptp90) REVERT: C 132 MET cc_start: 0.9115 (tmm) cc_final: 0.8447 (tmm) REVERT: E 305 MET cc_start: 0.9126 (mmm) cc_final: 0.8836 (mmm) REVERT: F 180 LEU cc_start: 0.9325 (tp) cc_final: 0.9113 (tp) REVERT: F 192 ILE cc_start: 0.9396 (pt) cc_final: 0.9182 (mt) REVERT: G 283 MET cc_start: 0.8989 (ppp) cc_final: 0.8786 (ppp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1176 time to fit residues: 32.1654 Evaluate side-chains 139 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 ASN F 12 ASN F 162 ASN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.042004 restraints weight = 75436.874| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.46 r_work: 0.2650 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20972 Z= 0.203 Angle : 0.648 9.430 28463 Z= 0.316 Chirality : 0.046 0.163 3161 Planarity : 0.005 0.055 3639 Dihedral : 9.663 175.605 2921 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.41 % Allowed : 4.33 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.17), residues: 2566 helix: -0.26 (0.16), residues: 1063 sheet: -0.02 (0.24), residues: 439 loop : 0.16 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 254 TYR 0.025 0.001 TYR E 279 PHE 0.024 0.002 PHE G 223 TRP 0.010 0.001 TRP C 340 HIS 0.006 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00458 (20972) covalent geometry : angle 0.64816 (28463) hydrogen bonds : bond 0.03563 ( 904) hydrogen bonds : angle 4.91946 ( 2412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 361 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9094 (mp0) REVERT: B 372 ARG cc_start: 0.8537 (ptp90) cc_final: 0.8168 (ptp90) REVERT: C 132 MET cc_start: 0.8530 (tmm) cc_final: 0.8272 (tmm) REVERT: C 355 MET cc_start: 0.9578 (mtp) cc_final: 0.9324 (mtm) REVERT: D 123 MET cc_start: 0.9128 (tpp) cc_final: 0.8910 (mmm) REVERT: E 305 MET cc_start: 0.9164 (mmm) cc_final: 0.8834 (mmm) REVERT: F 82 MET cc_start: 0.8814 (mmm) cc_final: 0.8141 (tmm) REVERT: F 123 MET cc_start: 0.9334 (mmm) cc_final: 0.8544 (mmm) REVERT: G 123 MET cc_start: 0.8914 (tpt) cc_final: 0.8700 (tpp) outliers start: 9 outliers final: 6 residues processed: 143 average time/residue: 0.1176 time to fit residues: 27.4145 Evaluate side-chains 141 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain E residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 67 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 41 optimal weight: 0.0370 chunk 55 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 overall best weight: 1.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 173 HIS ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.042561 restraints weight = 75263.104| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.42 r_work: 0.2656 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20972 Z= 0.137 Angle : 0.571 7.382 28463 Z= 0.274 Chirality : 0.044 0.171 3161 Planarity : 0.004 0.043 3639 Dihedral : 7.552 143.094 2921 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.50 % Allowed : 5.74 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2566 helix: 0.62 (0.16), residues: 1053 sheet: 0.21 (0.25), residues: 427 loop : 0.34 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 147 TYR 0.023 0.001 TYR E 279 PHE 0.015 0.001 PHE G 124 TRP 0.011 0.001 TRP D 340 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00312 (20972) covalent geometry : angle 0.57061 (28463) hydrogen bonds : bond 0.02923 ( 904) hydrogen bonds : angle 4.41875 ( 2412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8500 (tmm) cc_final: 0.8007 (tmm) REVERT: B 372 ARG cc_start: 0.8513 (ptp90) cc_final: 0.8228 (ptp90) REVERT: C 132 MET cc_start: 0.8733 (tmm) cc_final: 0.8318 (tmm) REVERT: C 355 MET cc_start: 0.9538 (mtp) cc_final: 0.9256 (mtm) REVERT: D 123 MET cc_start: 0.9109 (tpp) cc_final: 0.8847 (mmm) REVERT: E 47 MET cc_start: 0.7754 (pmm) cc_final: 0.7299 (pmm) REVERT: E 305 MET cc_start: 0.9171 (mmm) cc_final: 0.8879 (mmm) REVERT: F 82 MET cc_start: 0.8872 (mmm) cc_final: 0.8221 (tmm) REVERT: F 123 MET cc_start: 0.9324 (mmm) cc_final: 0.8497 (mmm) REVERT: F 276 GLU cc_start: 0.8252 (pm20) cc_final: 0.7813 (pm20) outliers start: 11 outliers final: 6 residues processed: 149 average time/residue: 0.1233 time to fit residues: 29.4501 Evaluate side-chains 140 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 223 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.041982 restraints weight = 75224.497| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.40 r_work: 0.2630 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20972 Z= 0.152 Angle : 0.569 7.611 28463 Z= 0.272 Chirality : 0.044 0.158 3161 Planarity : 0.004 0.038 3639 Dihedral : 6.420 136.824 2921 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.55 % Allowed : 6.74 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.17), residues: 2566 helix: 0.99 (0.17), residues: 1049 sheet: 0.25 (0.25), residues: 437 loop : 0.27 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 372 TYR 0.019 0.001 TYR E 279 PHE 0.014 0.001 PHE G 124 TRP 0.011 0.001 TRP D 340 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00347 (20972) covalent geometry : angle 0.56863 (28463) hydrogen bonds : bond 0.02791 ( 904) hydrogen bonds : angle 4.34598 ( 2412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8523 (tmm) cc_final: 0.8085 (tmm) REVERT: B 372 ARG cc_start: 0.8534 (ptp90) cc_final: 0.8103 (ptp90) REVERT: C 132 MET cc_start: 0.8626 (tmm) cc_final: 0.8399 (tmm) REVERT: D 123 MET cc_start: 0.9176 (tpp) cc_final: 0.8858 (mmm) REVERT: E 305 MET cc_start: 0.9133 (mmm) cc_final: 0.8917 (mmm) REVERT: F 82 MET cc_start: 0.8906 (mmm) cc_final: 0.8172 (tmm) REVERT: F 123 MET cc_start: 0.9354 (mmm) cc_final: 0.8495 (mmm) REVERT: F 276 GLU cc_start: 0.8199 (pm20) cc_final: 0.7789 (pm20) REVERT: G 44 MET cc_start: 0.9447 (mmm) cc_final: 0.9167 (mmm) REVERT: G 323 SER cc_start: 0.8812 (p) cc_final: 0.8586 (t) outliers start: 12 outliers final: 7 residues processed: 146 average time/residue: 0.1214 time to fit residues: 28.4551 Evaluate side-chains 142 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 136 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 HIS ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.053444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.040686 restraints weight = 75703.450| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.38 r_work: 0.2593 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20972 Z= 0.215 Angle : 0.606 7.455 28463 Z= 0.293 Chirality : 0.046 0.176 3161 Planarity : 0.004 0.036 3639 Dihedral : 6.234 135.653 2921 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.77 % Allowed : 7.70 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.17), residues: 2566 helix: 1.23 (0.17), residues: 1044 sheet: 0.26 (0.24), residues: 462 loop : 0.27 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 372 TYR 0.016 0.001 TYR E 279 PHE 0.011 0.001 PHE C 124 TRP 0.012 0.002 TRP D 340 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00490 (20972) covalent geometry : angle 0.60633 (28463) hydrogen bonds : bond 0.03078 ( 904) hydrogen bonds : angle 4.42062 ( 2412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8045 (mtp) REVERT: B 132 MET cc_start: 0.9138 (tmm) cc_final: 0.8622 (tmm) REVERT: B 355 MET cc_start: 0.9141 (mtm) cc_final: 0.8813 (ptp) REVERT: B 372 ARG cc_start: 0.8576 (ptp90) cc_final: 0.8294 (ptp90) REVERT: C 132 MET cc_start: 0.8640 (tmm) cc_final: 0.8429 (tmm) REVERT: D 123 MET cc_start: 0.9276 (tpp) cc_final: 0.8943 (mmm) REVERT: E 305 MET cc_start: 0.9196 (mmm) cc_final: 0.8922 (mmm) REVERT: F 82 MET cc_start: 0.8991 (mmm) cc_final: 0.8379 (tmm) REVERT: F 123 MET cc_start: 0.9400 (mmm) cc_final: 0.8516 (mmm) REVERT: F 276 GLU cc_start: 0.8247 (pm20) cc_final: 0.7825 (pm20) REVERT: F 355 MET cc_start: 0.9089 (mmm) cc_final: 0.8746 (mmm) REVERT: G 44 MET cc_start: 0.9452 (mmm) cc_final: 0.8980 (mmm) REVERT: G 123 MET cc_start: 0.8707 (tpt) cc_final: 0.8174 (tpp) REVERT: G 323 SER cc_start: 0.8835 (p) cc_final: 0.8623 (t) outliers start: 17 outliers final: 10 residues processed: 147 average time/residue: 0.1244 time to fit residues: 29.3730 Evaluate side-chains 147 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 238 optimal weight: 0.0270 chunk 15 optimal weight: 2.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 173 HIS D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.053420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.040685 restraints weight = 75543.022| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.38 r_work: 0.2593 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20972 Z= 0.196 Angle : 0.592 8.540 28463 Z= 0.285 Chirality : 0.046 0.173 3161 Planarity : 0.004 0.034 3639 Dihedral : 6.128 134.500 2921 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.87 % Allowed : 8.20 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.17), residues: 2566 helix: 1.26 (0.17), residues: 1040 sheet: 0.19 (0.24), residues: 472 loop : 0.33 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 372 TYR 0.014 0.001 TYR E 279 PHE 0.010 0.001 PHE G 223 TRP 0.012 0.002 TRP D 340 HIS 0.003 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00448 (20972) covalent geometry : angle 0.59236 (28463) hydrogen bonds : bond 0.02933 ( 904) hydrogen bonds : angle 4.37378 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7790 (mtp) REVERT: B 132 MET cc_start: 0.9073 (tmm) cc_final: 0.8557 (tmm) REVERT: B 325 MET cc_start: 0.7305 (mtt) cc_final: 0.7042 (mtt) REVERT: B 355 MET cc_start: 0.9129 (mtm) cc_final: 0.8659 (ptp) REVERT: B 372 ARG cc_start: 0.8581 (ptp90) cc_final: 0.8304 (ptp90) REVERT: D 123 MET cc_start: 0.9312 (tpp) cc_final: 0.8973 (mmm) REVERT: E 305 MET cc_start: 0.9190 (mmm) cc_final: 0.8951 (mmm) REVERT: F 82 MET cc_start: 0.9008 (mmm) cc_final: 0.8354 (tmm) REVERT: F 123 MET cc_start: 0.9398 (mmm) cc_final: 0.8487 (mmm) REVERT: F 276 GLU cc_start: 0.8199 (pm20) cc_final: 0.7814 (pm20) REVERT: F 355 MET cc_start: 0.9134 (mmm) cc_final: 0.8847 (mmm) REVERT: G 44 MET cc_start: 0.9418 (mmm) cc_final: 0.8782 (mmm) REVERT: G 124 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8051 (t80) outliers start: 19 outliers final: 9 residues processed: 146 average time/residue: 0.1109 time to fit residues: 26.5188 Evaluate side-chains 144 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 77 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 238 optimal weight: 8.9990 chunk 206 optimal weight: 0.0370 chunk 253 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 12 ASN D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.042175 restraints weight = 74681.620| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.37 r_work: 0.2634 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20972 Z= 0.097 Angle : 0.545 10.409 28463 Z= 0.258 Chirality : 0.044 0.164 3161 Planarity : 0.003 0.035 3639 Dihedral : 5.859 128.645 2921 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.55 % Allowed : 8.70 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.17), residues: 2566 helix: 1.36 (0.17), residues: 1048 sheet: 0.35 (0.25), residues: 462 loop : 0.43 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 372 TYR 0.027 0.001 TYR E 279 PHE 0.009 0.001 PHE G 223 TRP 0.012 0.001 TRP D 340 HIS 0.002 0.000 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00224 (20972) covalent geometry : angle 0.54533 (28463) hydrogen bonds : bond 0.02474 ( 904) hydrogen bonds : angle 4.13559 ( 2412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8732 (tmm) cc_final: 0.8234 (tmm) REVERT: A 325 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7816 (mtp) REVERT: B 132 MET cc_start: 0.8950 (tmm) cc_final: 0.8559 (tmm) REVERT: B 355 MET cc_start: 0.9115 (mtm) cc_final: 0.8744 (ptp) REVERT: B 372 ARG cc_start: 0.8592 (ptp90) cc_final: 0.8297 (ptp90) REVERT: D 47 MET cc_start: 0.8839 (pmm) cc_final: 0.8595 (pmm) REVERT: D 123 MET cc_start: 0.9265 (tpp) cc_final: 0.8892 (mmm) REVERT: D 184 ASP cc_start: 0.9143 (m-30) cc_final: 0.8871 (m-30) REVERT: D 372 ARG cc_start: 0.9355 (mtp-110) cc_final: 0.8866 (mtm-85) REVERT: E 305 MET cc_start: 0.9162 (mmm) cc_final: 0.8902 (mmm) REVERT: F 82 MET cc_start: 0.8886 (mmm) cc_final: 0.8287 (tmm) REVERT: F 123 MET cc_start: 0.9366 (mmm) cc_final: 0.8449 (mmm) REVERT: F 276 GLU cc_start: 0.8183 (pm20) cc_final: 0.7778 (pm20) REVERT: G 44 MET cc_start: 0.9398 (mmm) cc_final: 0.8747 (mmm) REVERT: G 124 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8080 (t80) REVERT: G 325 MET cc_start: 0.6611 (ptp) cc_final: 0.5431 (pmm) outliers start: 12 outliers final: 6 residues processed: 146 average time/residue: 0.1221 time to fit residues: 29.4988 Evaluate side-chains 143 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 18 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.054581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.041810 restraints weight = 75266.892| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.37 r_work: 0.2623 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20972 Z= 0.128 Angle : 0.557 10.478 28463 Z= 0.263 Chirality : 0.044 0.164 3161 Planarity : 0.003 0.037 3639 Dihedral : 5.765 125.853 2921 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.41 % Allowed : 9.34 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.17), residues: 2566 helix: 1.38 (0.17), residues: 1052 sheet: 0.38 (0.25), residues: 462 loop : 0.47 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 372 TYR 0.023 0.001 TYR E 279 PHE 0.008 0.001 PHE B 255 TRP 0.011 0.001 TRP D 340 HIS 0.002 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00297 (20972) covalent geometry : angle 0.55718 (28463) hydrogen bonds : bond 0.02587 ( 904) hydrogen bonds : angle 4.13367 ( 2412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8745 (tmm) cc_final: 0.8272 (tmm) REVERT: A 325 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7912 (mtp) REVERT: B 132 MET cc_start: 0.8972 (tmm) cc_final: 0.8545 (tmm) REVERT: B 372 ARG cc_start: 0.8599 (ptp90) cc_final: 0.8300 (ptp90) REVERT: D 123 MET cc_start: 0.9290 (tpp) cc_final: 0.8954 (mmm) REVERT: D 184 ASP cc_start: 0.9152 (m-30) cc_final: 0.8907 (m-30) REVERT: D 372 ARG cc_start: 0.9354 (mtp-110) cc_final: 0.8912 (mtm-85) REVERT: E 305 MET cc_start: 0.9197 (mmm) cc_final: 0.8863 (mmm) REVERT: F 82 MET cc_start: 0.8916 (mmm) cc_final: 0.8273 (tmm) REVERT: F 123 MET cc_start: 0.9405 (mmm) cc_final: 0.8462 (mmm) REVERT: F 276 GLU cc_start: 0.8173 (pm20) cc_final: 0.7814 (pm20) REVERT: G 44 MET cc_start: 0.9387 (mmm) cc_final: 0.8647 (mmm) REVERT: G 176 MET cc_start: 0.7949 (ptp) cc_final: 0.7489 (pmm) outliers start: 9 outliers final: 7 residues processed: 140 average time/residue: 0.1292 time to fit residues: 29.6964 Evaluate side-chains 142 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 71 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.041717 restraints weight = 74916.780| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.35 r_work: 0.2621 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20972 Z= 0.136 Angle : 0.561 10.781 28463 Z= 0.265 Chirality : 0.044 0.167 3161 Planarity : 0.003 0.037 3639 Dihedral : 5.702 122.310 2921 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.55 % Allowed : 9.29 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.18), residues: 2566 helix: 1.41 (0.17), residues: 1051 sheet: 0.38 (0.25), residues: 462 loop : 0.50 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 254 TYR 0.022 0.001 TYR E 279 PHE 0.008 0.001 PHE C 127 TRP 0.011 0.001 TRP D 340 HIS 0.003 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00314 (20972) covalent geometry : angle 0.56120 (28463) hydrogen bonds : bond 0.02620 ( 904) hydrogen bonds : angle 4.13323 ( 2412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8807 (tmm) cc_final: 0.8331 (tmm) REVERT: A 325 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7921 (mtp) REVERT: B 132 MET cc_start: 0.8959 (tmm) cc_final: 0.8535 (tmm) REVERT: B 372 ARG cc_start: 0.8642 (ptp90) cc_final: 0.8354 (ptp90) REVERT: D 47 MET cc_start: 0.8887 (pmm) cc_final: 0.8588 (pmm) REVERT: D 123 MET cc_start: 0.9294 (tpp) cc_final: 0.8956 (mmm) REVERT: D 184 ASP cc_start: 0.9149 (m-30) cc_final: 0.8910 (m-30) REVERT: D 372 ARG cc_start: 0.9365 (mtp-110) cc_final: 0.8931 (mtm-85) REVERT: E 305 MET cc_start: 0.9187 (mmm) cc_final: 0.8839 (mmm) REVERT: F 82 MET cc_start: 0.8950 (mmm) cc_final: 0.8310 (tmm) REVERT: F 123 MET cc_start: 0.9412 (mmm) cc_final: 0.8474 (mmm) REVERT: F 276 GLU cc_start: 0.8171 (pm20) cc_final: 0.7821 (pm20) REVERT: G 44 MET cc_start: 0.9376 (mmm) cc_final: 0.8607 (mmm) outliers start: 12 outliers final: 7 residues processed: 140 average time/residue: 0.1374 time to fit residues: 31.4700 Evaluate side-chains 142 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 199 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 150 optimal weight: 0.1980 chunk 222 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.054761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.042018 restraints weight = 75227.999| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.38 r_work: 0.2629 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20972 Z= 0.117 Angle : 0.557 11.363 28463 Z= 0.262 Chirality : 0.044 0.164 3161 Planarity : 0.003 0.037 3639 Dihedral : 5.583 114.902 2921 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.50 % Allowed : 9.38 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.18), residues: 2566 helix: 1.45 (0.17), residues: 1050 sheet: 0.46 (0.25), residues: 437 loop : 0.51 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 372 TYR 0.060 0.001 TYR A 279 PHE 0.007 0.001 PHE G 223 TRP 0.013 0.001 TRP G 356 HIS 0.002 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00270 (20972) covalent geometry : angle 0.55660 (28463) hydrogen bonds : bond 0.02555 ( 904) hydrogen bonds : angle 4.08868 ( 2412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8860 (tmm) cc_final: 0.8400 (tmm) REVERT: A 325 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7909 (mtp) REVERT: B 132 MET cc_start: 0.8930 (tmm) cc_final: 0.8540 (tmm) REVERT: B 372 ARG cc_start: 0.8659 (ptp90) cc_final: 0.8366 (ptp90) REVERT: D 123 MET cc_start: 0.9262 (tpp) cc_final: 0.8928 (mmm) REVERT: D 184 ASP cc_start: 0.9149 (m-30) cc_final: 0.8879 (m-30) REVERT: D 372 ARG cc_start: 0.9377 (mtp-110) cc_final: 0.8889 (mtm-85) REVERT: E 305 MET cc_start: 0.9197 (mmm) cc_final: 0.8863 (mmm) REVERT: F 82 MET cc_start: 0.8903 (mmm) cc_final: 0.8274 (tmm) REVERT: F 123 MET cc_start: 0.9367 (mmm) cc_final: 0.8447 (mmm) REVERT: F 276 GLU cc_start: 0.8200 (pm20) cc_final: 0.7830 (pm20) REVERT: G 44 MET cc_start: 0.9309 (mmm) cc_final: 0.8540 (mmm) outliers start: 11 outliers final: 8 residues processed: 141 average time/residue: 0.1373 time to fit residues: 31.4774 Evaluate side-chains 143 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 89 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.041957 restraints weight = 75349.070| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.37 r_work: 0.2628 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 20972 Z= 0.177 Angle : 0.722 59.200 28463 Z= 0.397 Chirality : 0.048 1.018 3161 Planarity : 0.003 0.065 3639 Dihedral : 5.604 114.877 2921 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 0.41 % Allowed : 9.25 % Favored : 90.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.17), residues: 2566 helix: 1.42 (0.17), residues: 1050 sheet: 0.44 (0.25), residues: 437 loop : 0.51 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 210 TYR 0.057 0.001 TYR A 279 PHE 0.007 0.001 PHE B 255 TRP 0.012 0.001 TRP G 356 HIS 0.003 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00382 (20972) covalent geometry : angle 0.72242 (28463) hydrogen bonds : bond 0.02609 ( 904) hydrogen bonds : angle 4.09109 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.47 seconds wall clock time: 51 minutes 51.71 seconds (3111.71 seconds total)