Starting phenix.real_space_refine on Thu Mar 5 19:19:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uuw_26805/03_2026/7uuw_26805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uuw_26805/03_2026/7uuw_26805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uuw_26805/03_2026/7uuw_26805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uuw_26805/03_2026/7uuw_26805.map" model { file = "/net/cci-nas-00/data/ceres_data/7uuw_26805/03_2026/7uuw_26805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uuw_26805/03_2026/7uuw_26805.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 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 12 5.49 5 Mg 6 5.21 5 S 192 5.16 5 C 15654 2.51 5 N 4242 2.21 5 O 4746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24852 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "H" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "I" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "K" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "L" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "Z" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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} Time building chain proxies: 5.45, per 1000 atoms: 0.22 Number of scatterers: 24852 At special positions: 0 Unit cell: (102.384, 120.528, 222.912, 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 192 16.00 P 12 15.00 Mg 6 11.99 O 4746 8.00 N 4242 7.00 C 15654 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: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 36 sheets defined 59.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.762A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.513A pdb=" N LEU A 65 " --> pdb=" O ARG A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.781A 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 194 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 284 through 285 No H-bonds generated for 'chain 'A' and resid 284 through 285' Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.892A 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 368 through 374 removed outlier: 4.068A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.513A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.780A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.784A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 284 through 285 No H-bonds generated for 'chain 'B' and resid 284 through 285' Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.581A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 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 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.737A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.892A 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: 4.068A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.582A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.780A 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 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 284 through 285 No H-bonds generated for 'chain 'C' and resid 284 through 285' Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.590A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.892A 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: 4.068A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU D 65 " --> pdb=" O ARG D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.780A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 257' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.581A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.892A 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: 4.069A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU E 65 " --> pdb=" O ARG E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.781A 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 194 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 257' Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 284 through 285 No H-bonds generated for 'chain 'E' and resid 284 through 285' Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.581A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 319 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.893A 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 374 removed outlier: 4.068A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU F 65 " --> pdb=" O ARG F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.781A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.782A pdb=" N ARG F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 257' Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.588A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 319 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.067A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 691 through 696 Processing helix chain 'G' and resid 714 through 738 Processing helix chain 'G' and resid 744 through 773 Processing helix chain 'G' and resid 776 through 810 removed outlier: 3.621A pdb=" N LYS G 780 " --> pdb=" O SER G 776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 810 " --> pdb=" O VAL G 806 " (cutoff:3.500A) Processing helix chain 'G' and resid 818 through 848 removed outlier: 4.250A pdb=" N SER G 823 " --> pdb=" O ASP G 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN G 837 " --> pdb=" O THR G 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR G 838 " --> pdb=" O ALA G 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS G 840 " --> pdb=" O VAL G 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 841 " --> pdb=" O GLN G 837 " (cutoff:3.500A) Processing helix chain 'H' and resid 691 through 696 Processing helix chain 'H' and resid 714 through 738 Processing helix chain 'H' and resid 744 through 773 Processing helix chain 'H' and resid 776 through 810 removed outlier: 3.621A pdb=" N LYS H 780 " --> pdb=" O SER H 776 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY H 810 " --> pdb=" O VAL H 806 " (cutoff:3.500A) Processing helix chain 'H' and resid 818 through 848 removed outlier: 4.252A pdb=" N SER H 823 " --> pdb=" O ASP H 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU H 824 " --> pdb=" O SER H 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN H 837 " --> pdb=" O THR H 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR H 838 " --> pdb=" O ALA H 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS H 840 " --> pdb=" O VAL H 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA H 841 " --> pdb=" O GLN H 837 " (cutoff:3.500A) Processing helix chain 'I' and resid 691 through 696 Processing helix chain 'I' and resid 714 through 738 Processing helix chain 'I' and resid 744 through 773 Processing helix chain 'I' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS I 780 " --> pdb=" O SER I 776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY I 810 " --> pdb=" O VAL I 806 " (cutoff:3.500A) Processing helix chain 'I' and resid 818 through 848 removed outlier: 4.251A pdb=" N SER I 823 " --> pdb=" O ASP I 819 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU I 824 " --> pdb=" O SER I 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN I 837 " --> pdb=" O THR I 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR I 838 " --> pdb=" O ALA I 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS I 840 " --> pdb=" O VAL I 836 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA I 841 " --> pdb=" O GLN I 837 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 696 Processing helix chain 'K' and resid 714 through 738 Processing helix chain 'K' and resid 744 through 773 Processing helix chain 'K' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS K 780 " --> pdb=" O SER K 776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY K 810 " --> pdb=" O VAL K 806 " (cutoff:3.500A) Processing helix chain 'K' and resid 818 through 848 removed outlier: 4.251A pdb=" N SER K 823 " --> pdb=" O ASP K 819 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU K 824 " --> pdb=" O SER K 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN K 837 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR K 838 " --> pdb=" O ALA K 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS K 840 " --> pdb=" O VAL K 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 841 " --> pdb=" O GLN K 837 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 696 Processing helix chain 'L' and resid 714 through 738 Processing helix chain 'L' and resid 744 through 773 Processing helix chain 'L' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS L 780 " --> pdb=" O SER L 776 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY L 810 " --> pdb=" O VAL L 806 " (cutoff:3.500A) Processing helix chain 'L' and resid 818 through 848 removed outlier: 4.250A pdb=" N SER L 823 " --> pdb=" O ASP L 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU L 824 " --> pdb=" O SER L 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN L 837 " --> pdb=" O THR L 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR L 838 " --> pdb=" O ALA L 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS L 840 " --> pdb=" O VAL L 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 841 " --> pdb=" O GLN L 837 " (cutoff:3.500A) Processing helix chain 'Z' and resid 691 through 696 Processing helix chain 'Z' and resid 714 through 738 Processing helix chain 'Z' and resid 744 through 773 Processing helix chain 'Z' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS Z 780 " --> pdb=" O SER Z 776 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY Z 810 " --> pdb=" O VAL Z 806 " (cutoff:3.500A) Processing helix chain 'Z' and resid 818 through 848 removed outlier: 4.251A pdb=" N SER Z 823 " --> pdb=" O ASP Z 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU Z 824 " --> pdb=" O SER Z 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN Z 837 " --> pdb=" O THR Z 833 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR Z 838 " --> pdb=" O ALA Z 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS Z 840 " --> pdb=" O VAL Z 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Z 841 " --> pdb=" O GLN Z 837 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.064A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.521A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.129A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.520A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (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: 7.064A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.550A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 7.130A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (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: 7.064A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.510A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 7.065A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AC2, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.528A pdb=" N GLN D 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL F 298 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 32 removed outlier: 7.065A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC7, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC9, first strand: chain 'F' and resid 29 through 32 removed outlier: 7.065A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AD2, first strand: chain 'F' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET F 176 " --> pdb=" O ASN F 162 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'G' and resid 697 through 698 Processing sheet with id=AD5, first strand: chain 'H' and resid 697 through 698 Processing sheet with id=AD6, first strand: chain 'I' and resid 697 through 698 Processing sheet with id=AD7, first strand: chain 'K' and resid 697 through 698 Processing sheet with id=AD8, first strand: chain 'L' and resid 697 through 698 Processing sheet with id=AD9, first strand: chain 'Z' and resid 697 through 698 1300 hydrogen bonds defined for protein. 3684 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: 4.60 Time building geometry restraints manager: 2.97 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: 8112 1.34 - 1.46: 5463 1.46 - 1.58: 11373 1.58 - 1.70: 18 1.70 - 1.82: 330 Bond restraints: 25296 Sorted by residual: bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.19e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.15e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.11e+00 ... (remaining 25291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 33806 2.78 - 5.57: 409 5.57 - 8.35: 15 8.35 - 11.13: 0 11.13 - 13.92: 12 Bond angle restraints: 34242 Sorted by residual: angle pdb=" CB MET F 325 " pdb=" CG MET F 325 " pdb=" SD MET F 325 " ideal model delta sigma weight residual 112.70 98.78 13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 98.80 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 98.80 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET C 325 " pdb=" CG MET C 325 " pdb=" SD MET C 325 " ideal model delta sigma weight residual 112.70 98.81 13.89 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " ideal model delta sigma weight residual 112.70 98.81 13.89 3.00e+00 1.11e-01 2.14e+01 ... (remaining 34237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 14910 34.41 - 68.82: 444 68.82 - 103.24: 48 103.24 - 137.65: 6 137.65 - 172.06: 12 Dihedral angle restraints: 15420 sinusoidal: 6222 harmonic: 9198 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.06 -172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.06 -172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.04 -172.04 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 15417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2192 0.034 - 0.068: 1232 0.068 - 0.103: 352 0.103 - 0.137: 113 0.137 - 0.171: 23 Chirality restraints: 3912 Sorted by residual: chirality pdb=" CA MET E 325 " pdb=" N MET E 325 " pdb=" C MET E 325 " pdb=" CB MET E 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA MET C 325 " pdb=" N MET C 325 " pdb=" C MET C 325 " pdb=" CB MET C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA MET B 325 " pdb=" N MET B 325 " pdb=" C MET B 325 " pdb=" CB MET B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 3909 not shown) Planarity restraints: 4338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO E 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO D 243 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.022 5.00e-02 4.00e+02 ... (remaining 4335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2987 2.74 - 3.28: 24061 3.28 - 3.82: 39496 3.82 - 4.36: 49656 4.36 - 4.90: 88228 Nonbonded interactions: 204428 Sorted by model distance: nonbonded pdb=" O GLY A 156 " pdb=" OG1 THR A 303 " model vdw 2.202 3.040 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.203 3.040 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.203 3.040 nonbonded pdb=" O GLY C 156 " pdb=" OG1 THR C 303 " model vdw 2.203 3.040 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.204 3.040 ... (remaining 204423 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.590 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.007 0.054 25296 Z= 0.293 Angle : 0.750 13.916 34242 Z= 0.392 Chirality : 0.046 0.171 3912 Planarity : 0.004 0.040 4338 Dihedral : 17.000 172.062 9480 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.34 % Allowed : 3.53 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3096 helix: 0.48 (0.13), residues: 1656 sheet: -1.68 (0.27), residues: 366 loop : -0.22 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 206 TYR 0.014 0.002 TYR D 279 PHE 0.013 0.001 PHE Z 697 TRP 0.018 0.002 TRP A 340 HIS 0.003 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00704 (25296) covalent geometry : angle 0.74983 (34242) hydrogen bonds : bond 0.15765 ( 1300) hydrogen bonds : angle 6.68532 ( 3684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 329 time to evaluate : 0.926 Fit side-chains REVERT: A 118 LYS cc_start: 0.8375 (mttm) cc_final: 0.7907 (mmmt) REVERT: A 119 MET cc_start: 0.8288 (mtm) cc_final: 0.7659 (mtp) REVERT: A 157 ASP cc_start: 0.8839 (t0) cc_final: 0.8516 (t70) REVERT: A 176 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8124 (mtt) REVERT: A 211 ASP cc_start: 0.8634 (t0) cc_final: 0.8250 (t0) REVERT: A 227 MET cc_start: 0.8660 (mmm) cc_final: 0.8232 (mmt) REVERT: B 123 MET cc_start: 0.8667 (mmt) cc_final: 0.8386 (mmm) REVERT: B 191 LYS cc_start: 0.7348 (tttp) cc_final: 0.6910 (tttt) REVERT: B 313 MET cc_start: 0.8219 (ttt) cc_final: 0.7839 (ttt) REVERT: B 349 LEU cc_start: 0.8477 (mt) cc_final: 0.8178 (mt) REVERT: C 82 MET cc_start: 0.8551 (tpt) cc_final: 0.8341 (tpt) REVERT: C 211 ASP cc_start: 0.8594 (t0) cc_final: 0.8265 (t0) REVERT: C 313 MET cc_start: 0.8000 (ttt) cc_final: 0.7738 (ttm) REVERT: D 119 MET cc_start: 0.8108 (mtm) cc_final: 0.7900 (mtm) REVERT: D 313 MET cc_start: 0.8358 (ttt) cc_final: 0.7941 (ttt) REVERT: D 325 MET cc_start: 0.8022 (mmt) cc_final: 0.7807 (mmt) REVERT: E 100 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7636 (mt-10) REVERT: E 118 LYS cc_start: 0.8579 (mttm) cc_final: 0.8073 (mmmt) REVERT: E 123 MET cc_start: 0.8764 (mmt) cc_final: 0.8548 (mmt) REVERT: E 292 ASP cc_start: 0.7332 (m-30) cc_final: 0.7125 (m-30) REVERT: F 57 GLU cc_start: 0.8328 (pt0) cc_final: 0.8036 (pt0) REVERT: F 157 ASP cc_start: 0.9022 (t0) cc_final: 0.8814 (t0) REVERT: F 299 MET cc_start: 0.8766 (mtm) cc_final: 0.8554 (mtp) REVERT: G 746 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7198 (mmm) REVERT: G 863 MET cc_start: 0.7720 (mtm) cc_final: 0.7192 (ttm) REVERT: H 725 MET cc_start: 0.7749 (mtt) cc_final: 0.7350 (mtt) REVERT: H 822 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8179 (mmp) REVERT: I 732 MET cc_start: 0.8281 (mtp) cc_final: 0.8018 (mtp) REVERT: K 869 GLN cc_start: 0.8795 (mm110) cc_final: 0.8501 (mm-40) REVERT: L 732 MET cc_start: 0.8189 (mtp) cc_final: 0.7968 (mtm) REVERT: L 746 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7454 (tpt) REVERT: L 794 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8340 (tp40) REVERT: Z 732 MET cc_start: 0.8243 (mtp) cc_final: 0.7921 (mtp) REVERT: Z 746 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7559 (mmm) REVERT: Z 794 GLN cc_start: 0.9079 (tp40) cc_final: 0.8828 (tp40) REVERT: Z 822 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7689 (mmm) outliers start: 36 outliers final: 7 residues processed: 335 average time/residue: 0.1628 time to fit residues: 88.2718 Evaluate side-chains 270 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 257 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain G residue 746 MET Chi-restraints excluded: chain H residue 822 MET Chi-restraints excluded: chain L residue 746 MET Chi-restraints excluded: chain Z residue 746 MET Chi-restraints excluded: chain Z residue 822 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 353 GLN K 794 GLN L 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.111041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.091249 restraints weight = 27318.933| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 0.98 r_work: 0.2742 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25296 Z= 0.131 Angle : 0.553 7.861 34242 Z= 0.276 Chirality : 0.041 0.156 3912 Planarity : 0.004 0.037 4338 Dihedral : 12.048 170.497 3511 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.82 % Allowed : 6.21 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 3096 helix: 1.13 (0.13), residues: 1686 sheet: -1.28 (0.27), residues: 378 loop : -0.09 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 206 TYR 0.011 0.001 TYR F 143 PHE 0.008 0.001 PHE B 127 TRP 0.015 0.001 TRP E 340 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00296 (25296) covalent geometry : angle 0.55321 (34242) hydrogen bonds : bond 0.04824 ( 1300) hydrogen bonds : angle 4.87885 ( 3684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 277 time to evaluate : 0.979 Fit side-chains REVERT: A 118 LYS cc_start: 0.8204 (mttm) cc_final: 0.7661 (mmmt) REVERT: A 119 MET cc_start: 0.8182 (mtm) cc_final: 0.7878 (mtp) REVERT: A 157 ASP cc_start: 0.8938 (t0) cc_final: 0.8721 (t0) REVERT: B 66 THR cc_start: 0.9282 (p) cc_final: 0.9071 (p) REVERT: B 123 MET cc_start: 0.8739 (mmt) cc_final: 0.8408 (mmm) REVERT: B 191 LYS cc_start: 0.7871 (tttp) cc_final: 0.7554 (tttt) REVERT: B 313 MET cc_start: 0.8314 (ttt) cc_final: 0.7895 (ttt) REVERT: B 326 LYS cc_start: 0.8243 (ttpp) cc_final: 0.8022 (tttp) REVERT: C 82 MET cc_start: 0.8574 (tpt) cc_final: 0.8350 (tpt) REVERT: C 211 ASP cc_start: 0.8746 (t0) cc_final: 0.8453 (t0) REVERT: D 191 LYS cc_start: 0.7779 (tttp) cc_final: 0.7385 (tptt) REVERT: D 311 ASP cc_start: 0.8021 (m-30) cc_final: 0.7805 (m-30) REVERT: D 313 MET cc_start: 0.8548 (ttt) cc_final: 0.8155 (ttt) REVERT: E 72 GLU cc_start: 0.7822 (tt0) cc_final: 0.7458 (tt0) REVERT: E 354 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7824 (pt0) REVERT: E 355 MET cc_start: 0.9246 (mtt) cc_final: 0.9028 (mtm) REVERT: F 44 MET cc_start: 0.8505 (mtt) cc_final: 0.8262 (mtp) REVERT: F 57 GLU cc_start: 0.8556 (pt0) cc_final: 0.8179 (pt0) REVERT: F 283 MET cc_start: 0.8554 (mmm) cc_final: 0.8321 (mmt) REVERT: G 805 ASP cc_start: 0.6878 (m-30) cc_final: 0.6478 (m-30) REVERT: G 863 MET cc_start: 0.8167 (mtm) cc_final: 0.7798 (mtp) REVERT: H 729 MET cc_start: 0.8379 (tpt) cc_final: 0.7592 (tpt) REVERT: H 822 MET cc_start: 0.8288 (mmm) cc_final: 0.8053 (mmm) REVERT: I 732 MET cc_start: 0.8298 (mtp) cc_final: 0.8033 (mtp) REVERT: I 822 MET cc_start: 0.8512 (mmm) cc_final: 0.7849 (mmt) REVERT: K 746 MET cc_start: 0.7877 (mmm) cc_final: 0.7381 (tpp) REVERT: L 729 MET cc_start: 0.7651 (tpt) cc_final: 0.7278 (tpt) REVERT: L 732 MET cc_start: 0.8267 (mtm) cc_final: 0.8002 (mtm) REVERT: L 746 MET cc_start: 0.7285 (tpp) cc_final: 0.6917 (tpt) REVERT: L 822 MET cc_start: 0.8498 (mmp) cc_final: 0.8232 (mmt) REVERT: Z 732 MET cc_start: 0.8307 (mtm) cc_final: 0.7965 (mtp) REVERT: Z 746 MET cc_start: 0.7673 (tpp) cc_final: 0.7463 (mmm) REVERT: Z 794 GLN cc_start: 0.9130 (tp40) cc_final: 0.8894 (tp40) outliers start: 22 outliers final: 17 residues processed: 289 average time/residue: 0.1542 time to fit residues: 73.7389 Evaluate side-chains 272 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 255 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 264 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 184 optimal weight: 0.0370 chunk 192 optimal weight: 0.6980 chunk 273 optimal weight: 5.9990 chunk 263 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 252 ASN L 837 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.107989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.087930 restraints weight = 27697.193| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 0.98 r_work: 0.2690 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25296 Z= 0.147 Angle : 0.532 6.647 34242 Z= 0.262 Chirality : 0.041 0.156 3912 Planarity : 0.003 0.035 4338 Dihedral : 10.358 148.463 3486 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.04 % Allowed : 7.51 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 3096 helix: 1.31 (0.13), residues: 1686 sheet: -1.28 (0.27), residues: 366 loop : -0.03 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 829 TYR 0.011 0.001 TYR E 143 PHE 0.008 0.001 PHE C 255 TRP 0.015 0.001 TRP E 340 HIS 0.003 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00351 (25296) covalent geometry : angle 0.53202 (34242) hydrogen bonds : bond 0.04633 ( 1300) hydrogen bonds : angle 4.59781 ( 3684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 1.035 Fit side-chains REVERT: A 72 GLU cc_start: 0.8096 (tt0) cc_final: 0.7409 (mt-10) REVERT: A 118 LYS cc_start: 0.8241 (mttm) cc_final: 0.7644 (mmmt) REVERT: A 119 MET cc_start: 0.7953 (mtm) cc_final: 0.7629 (mtp) REVERT: A 157 ASP cc_start: 0.8938 (t0) cc_final: 0.8703 (t0) REVERT: A 176 MET cc_start: 0.8622 (mmm) cc_final: 0.8365 (mmm) REVERT: B 66 THR cc_start: 0.9315 (p) cc_final: 0.9075 (p) REVERT: B 176 MET cc_start: 0.8415 (mtt) cc_final: 0.8043 (mtt) REVERT: B 191 LYS cc_start: 0.7802 (tttp) cc_final: 0.7459 (tttt) REVERT: B 305 MET cc_start: 0.8982 (mtp) cc_final: 0.8740 (mmm) REVERT: B 326 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8026 (tttp) REVERT: C 82 MET cc_start: 0.8589 (tpt) cc_final: 0.8363 (tpt) REVERT: C 195 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8266 (mt-10) REVERT: C 211 ASP cc_start: 0.8804 (t0) cc_final: 0.8500 (t0) REVERT: D 191 LYS cc_start: 0.7886 (tttp) cc_final: 0.7194 (tttt) REVERT: D 311 ASP cc_start: 0.8053 (m-30) cc_final: 0.7831 (m-30) REVERT: D 313 MET cc_start: 0.8556 (ttt) cc_final: 0.8325 (ttt) REVERT: D 354 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8170 (mm-40) REVERT: E 72 GLU cc_start: 0.7931 (tt0) cc_final: 0.7360 (tt0) REVERT: E 354 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7887 (pt0) REVERT: E 355 MET cc_start: 0.9196 (mtt) cc_final: 0.8990 (mtm) REVERT: F 57 GLU cc_start: 0.8583 (pt0) cc_final: 0.8134 (pt0) REVERT: F 325 MET cc_start: 0.8955 (mmp) cc_final: 0.8598 (mmp) REVERT: F 344 SER cc_start: 0.8655 (m) cc_final: 0.8296 (p) REVERT: G 805 ASP cc_start: 0.6902 (m-30) cc_final: 0.6422 (m-30) REVERT: G 863 MET cc_start: 0.8309 (mtm) cc_final: 0.7904 (mtp) REVERT: H 729 MET cc_start: 0.8274 (tpt) cc_final: 0.7406 (tpt) REVERT: I 732 MET cc_start: 0.8304 (mtp) cc_final: 0.7959 (mtp) REVERT: I 822 MET cc_start: 0.8553 (mmm) cc_final: 0.8010 (mmt) REVERT: K 746 MET cc_start: 0.7648 (mmm) cc_final: 0.7167 (tpp) REVERT: L 725 MET cc_start: 0.7058 (mtt) cc_final: 0.6844 (mtt) REVERT: L 746 MET cc_start: 0.7248 (tpp) cc_final: 0.6897 (tpt) REVERT: L 794 GLN cc_start: 0.8620 (tp40) cc_final: 0.8420 (tp40) REVERT: L 822 MET cc_start: 0.8443 (mmp) cc_final: 0.8199 (mmt) REVERT: Z 732 MET cc_start: 0.8317 (mtm) cc_final: 0.8071 (mtm) REVERT: Z 746 MET cc_start: 0.7599 (tpp) cc_final: 0.7396 (mmm) outliers start: 28 outliers final: 22 residues processed: 287 average time/residue: 0.1570 time to fit residues: 74.9280 Evaluate side-chains 278 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 252 ASN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 280 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 286 optimal weight: 0.0470 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 353 GLN K 794 GLN L 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.107445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.087451 restraints weight = 27571.847| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 0.98 r_work: 0.2725 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25296 Z= 0.170 Angle : 0.540 6.641 34242 Z= 0.265 Chirality : 0.042 0.148 3912 Planarity : 0.003 0.034 4338 Dihedral : 9.709 132.967 3480 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.04 % Allowed : 8.44 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 3096 helix: 1.29 (0.13), residues: 1692 sheet: -1.17 (0.28), residues: 330 loop : -0.09 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 829 TYR 0.011 0.001 TYR B 143 PHE 0.009 0.001 PHE C 255 TRP 0.015 0.001 TRP E 340 HIS 0.003 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00413 (25296) covalent geometry : angle 0.54048 (34242) hydrogen bonds : bond 0.04606 ( 1300) hydrogen bonds : angle 4.54611 ( 3684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.941 Fit side-chains REVERT: A 72 GLU cc_start: 0.7919 (tt0) cc_final: 0.7296 (mt-10) REVERT: A 118 LYS cc_start: 0.8237 (mttm) cc_final: 0.7643 (mmmt) REVERT: A 119 MET cc_start: 0.7860 (mtm) cc_final: 0.7549 (mtp) REVERT: A 176 MET cc_start: 0.8707 (mmm) cc_final: 0.8484 (mmm) REVERT: A 369 ILE cc_start: 0.8494 (tp) cc_final: 0.8238 (tp) REVERT: B 176 MET cc_start: 0.8338 (mtt) cc_final: 0.7981 (mtt) REVERT: B 191 LYS cc_start: 0.7856 (tttp) cc_final: 0.7499 (tttt) REVERT: B 305 MET cc_start: 0.8985 (mtp) cc_final: 0.8747 (mmm) REVERT: B 326 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7966 (tttp) REVERT: C 82 MET cc_start: 0.8521 (tpt) cc_final: 0.8304 (tpt) REVERT: C 211 ASP cc_start: 0.8857 (t0) cc_final: 0.8541 (t0) REVERT: D 132 MET cc_start: 0.8555 (ptm) cc_final: 0.8352 (ttp) REVERT: D 311 ASP cc_start: 0.8060 (m-30) cc_final: 0.7829 (m-30) REVERT: D 313 MET cc_start: 0.8576 (ttt) cc_final: 0.8344 (ttt) REVERT: E 72 GLU cc_start: 0.7877 (tt0) cc_final: 0.7289 (tt0) REVERT: E 118 LYS cc_start: 0.8583 (mttm) cc_final: 0.7933 (mmmt) REVERT: E 354 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7844 (pt0) REVERT: F 57 GLU cc_start: 0.8648 (pt0) cc_final: 0.8191 (pt0) REVERT: F 61 LYS cc_start: 0.8516 (mttm) cc_final: 0.8243 (mttm) REVERT: F 325 MET cc_start: 0.8987 (mmp) cc_final: 0.8742 (mmp) REVERT: G 863 MET cc_start: 0.8341 (mtm) cc_final: 0.7923 (mtp) REVERT: H 729 MET cc_start: 0.8296 (tpt) cc_final: 0.7463 (tpt) REVERT: I 732 MET cc_start: 0.8277 (mtp) cc_final: 0.7878 (mtp) REVERT: I 822 MET cc_start: 0.8510 (mmm) cc_final: 0.8080 (mmt) REVERT: I 863 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8006 (ttm) REVERT: L 729 MET cc_start: 0.7501 (tpt) cc_final: 0.7162 (tpt) REVERT: L 746 MET cc_start: 0.7152 (tpp) cc_final: 0.6790 (tpt) REVERT: Z 732 MET cc_start: 0.8286 (mtm) cc_final: 0.8054 (mtm) REVERT: Z 746 MET cc_start: 0.7542 (tpp) cc_final: 0.7304 (mmm) REVERT: Z 794 GLN cc_start: 0.8996 (tp40) cc_final: 0.8745 (tp40) outliers start: 28 outliers final: 23 residues processed: 271 average time/residue: 0.1585 time to fit residues: 71.5146 Evaluate side-chains 273 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain I residue 863 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS E 360 GLN I 837 GLN K 794 GLN L 794 GLN L 837 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.104879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.084887 restraints weight = 27918.855| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 0.93 r_work: 0.2646 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 25296 Z= 0.266 Angle : 0.619 7.025 34242 Z= 0.306 Chirality : 0.046 0.154 3912 Planarity : 0.004 0.035 4338 Dihedral : 9.580 137.401 3480 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.41 % Allowed : 9.11 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3096 helix: 1.01 (0.13), residues: 1692 sheet: -1.12 (0.27), residues: 342 loop : -0.21 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 206 TYR 0.015 0.002 TYR D 143 PHE 0.012 0.002 PHE C 255 TRP 0.018 0.002 TRP E 340 HIS 0.005 0.002 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00665 (25296) covalent geometry : angle 0.61942 (34242) hydrogen bonds : bond 0.05291 ( 1300) hydrogen bonds : angle 4.72422 ( 3684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.944 Fit side-chains REVERT: A 118 LYS cc_start: 0.8287 (mttm) cc_final: 0.7728 (mmmt) REVERT: A 119 MET cc_start: 0.7849 (mtm) cc_final: 0.7639 (mtp) REVERT: A 326 LYS cc_start: 0.8537 (tttp) cc_final: 0.8215 (tttm) REVERT: A 360 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: A 369 ILE cc_start: 0.8542 (tp) cc_final: 0.8282 (tp) REVERT: B 191 LYS cc_start: 0.8006 (tttp) cc_final: 0.7730 (tttt) REVERT: B 305 MET cc_start: 0.9021 (mtp) cc_final: 0.8818 (mmm) REVERT: C 211 ASP cc_start: 0.8922 (t0) cc_final: 0.8592 (t0) REVERT: D 132 MET cc_start: 0.8488 (ptm) cc_final: 0.8260 (ttp) REVERT: D 191 LYS cc_start: 0.8096 (tttp) cc_final: 0.7433 (ttmt) REVERT: D 313 MET cc_start: 0.8609 (ttt) cc_final: 0.8158 (ttt) REVERT: E 72 GLU cc_start: 0.8126 (tt0) cc_final: 0.7691 (tt0) REVERT: E 118 LYS cc_start: 0.8654 (mttm) cc_final: 0.8045 (mmmt) REVERT: E 354 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7839 (pt0) REVERT: F 57 GLU cc_start: 0.8504 (pt0) cc_final: 0.8204 (pt0) REVERT: F 61 LYS cc_start: 0.8579 (mttm) cc_final: 0.8283 (mttm) REVERT: G 863 MET cc_start: 0.8447 (mtm) cc_final: 0.7994 (mtp) REVERT: H 729 MET cc_start: 0.8452 (tpt) cc_final: 0.7681 (tpt) REVERT: I 732 MET cc_start: 0.8291 (mtp) cc_final: 0.8037 (mtp) REVERT: I 822 MET cc_start: 0.8639 (mmm) cc_final: 0.7956 (mmt) REVERT: I 863 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8249 (ttm) REVERT: I 869 GLN cc_start: 0.8965 (mm110) cc_final: 0.8558 (mm110) REVERT: L 729 MET cc_start: 0.7683 (tpt) cc_final: 0.7456 (tpt) REVERT: L 746 MET cc_start: 0.7214 (tpp) cc_final: 0.6848 (tpt) REVERT: Z 732 MET cc_start: 0.8368 (mtm) cc_final: 0.7985 (mtp) REVERT: Z 794 GLN cc_start: 0.8986 (tp40) cc_final: 0.8707 (tp40) outliers start: 38 outliers final: 32 residues processed: 276 average time/residue: 0.1631 time to fit residues: 73.2682 Evaluate side-chains 276 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain I residue 863 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 57 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 308 optimal weight: 0.9990 chunk 287 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS L 837 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.108450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.088104 restraints weight = 27444.787| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 0.97 r_work: 0.2697 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25296 Z= 0.120 Angle : 0.510 6.558 34242 Z= 0.249 Chirality : 0.040 0.159 3912 Planarity : 0.003 0.036 4338 Dihedral : 9.313 143.250 3480 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.15 % Allowed : 9.82 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 3096 helix: 1.38 (0.13), residues: 1692 sheet: -1.20 (0.27), residues: 330 loop : -0.03 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.009 0.001 TYR B 143 PHE 0.007 0.001 PHE F 31 TRP 0.015 0.001 TRP C 340 HIS 0.002 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00274 (25296) covalent geometry : angle 0.50979 (34242) hydrogen bonds : bond 0.04321 ( 1300) hydrogen bonds : angle 4.43025 ( 3684) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.902 Fit side-chains REVERT: A 118 LYS cc_start: 0.8275 (mttm) cc_final: 0.7681 (mmmt) REVERT: A 119 MET cc_start: 0.7784 (mtm) cc_final: 0.7568 (mtp) REVERT: A 191 LYS cc_start: 0.8193 (tttp) cc_final: 0.7587 (tttp) REVERT: A 326 LYS cc_start: 0.8512 (tttp) cc_final: 0.8193 (tttm) REVERT: A 360 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: A 369 ILE cc_start: 0.8521 (tp) cc_final: 0.8214 (tp) REVERT: B 191 LYS cc_start: 0.7941 (tttp) cc_final: 0.7469 (tttt) REVERT: B 305 MET cc_start: 0.8951 (mtp) cc_final: 0.8731 (mmm) REVERT: C 211 ASP cc_start: 0.8834 (t0) cc_final: 0.8515 (t0) REVERT: E 72 GLU cc_start: 0.7875 (tt0) cc_final: 0.7431 (tt0) REVERT: E 354 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7942 (pt0) REVERT: F 57 GLU cc_start: 0.8496 (pt0) cc_final: 0.8125 (pt0) REVERT: F 61 LYS cc_start: 0.8527 (mttm) cc_final: 0.8092 (mtpp) REVERT: H 729 MET cc_start: 0.8384 (tpt) cc_final: 0.7682 (tpt) REVERT: I 732 MET cc_start: 0.8293 (mtp) cc_final: 0.8051 (mtm) REVERT: I 822 MET cc_start: 0.8562 (mmm) cc_final: 0.7907 (mmt) REVERT: I 863 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7943 (ttm) REVERT: I 869 GLN cc_start: 0.8962 (mm110) cc_final: 0.8577 (mm110) REVERT: L 746 MET cc_start: 0.7099 (tpp) cc_final: 0.6679 (tpt) REVERT: Z 732 MET cc_start: 0.8302 (mtm) cc_final: 0.8067 (mtm) outliers start: 31 outliers final: 22 residues processed: 266 average time/residue: 0.1593 time to fit residues: 69.7685 Evaluate side-chains 267 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain I residue 863 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 134 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 HIS L 794 GLN Z 794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.109210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.089020 restraints weight = 27420.757| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 0.94 r_work: 0.2711 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25296 Z= 0.122 Angle : 0.500 6.457 34242 Z= 0.242 Chirality : 0.040 0.146 3912 Planarity : 0.003 0.033 4338 Dihedral : 8.945 143.780 3480 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.30 % Allowed : 10.12 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.16), residues: 3096 helix: 1.69 (0.13), residues: 1656 sheet: -0.95 (0.27), residues: 360 loop : 0.21 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 147 TYR 0.010 0.001 TYR C 188 PHE 0.007 0.001 PHE F 31 TRP 0.015 0.001 TRP E 340 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00283 (25296) covalent geometry : angle 0.50023 (34242) hydrogen bonds : bond 0.04121 ( 1300) hydrogen bonds : angle 4.30283 ( 3684) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8347 (mttm) cc_final: 0.7806 (mmmt) REVERT: A 119 MET cc_start: 0.7917 (mtm) cc_final: 0.7713 (mtp) REVERT: A 191 LYS cc_start: 0.8126 (tttp) cc_final: 0.7561 (tttp) REVERT: B 191 LYS cc_start: 0.8075 (tttp) cc_final: 0.7542 (tttt) REVERT: B 205 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7993 (mt-10) REVERT: B 305 MET cc_start: 0.8924 (mtp) cc_final: 0.8698 (mmm) REVERT: C 145 SER cc_start: 0.9184 (t) cc_final: 0.8859 (m) REVERT: C 211 ASP cc_start: 0.8819 (t0) cc_final: 0.8496 (t0) REVERT: C 253 GLU cc_start: 0.8946 (mp0) cc_final: 0.8598 (mp0) REVERT: E 72 GLU cc_start: 0.7896 (tt0) cc_final: 0.7372 (tt0) REVERT: E 354 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7962 (pt0) REVERT: F 57 GLU cc_start: 0.8468 (pt0) cc_final: 0.8179 (pt0) REVERT: F 344 SER cc_start: 0.8626 (m) cc_final: 0.8263 (p) REVERT: G 795 GLN cc_start: 0.9018 (mt0) cc_final: 0.8740 (mt0) REVERT: G 805 ASP cc_start: 0.6892 (m-30) cc_final: 0.6494 (m-30) REVERT: H 729 MET cc_start: 0.8412 (tpt) cc_final: 0.7742 (tpt) REVERT: H 794 GLN cc_start: 0.9036 (tp40) cc_final: 0.8712 (tp-100) REVERT: I 732 MET cc_start: 0.8231 (mtp) cc_final: 0.7984 (mtm) REVERT: I 805 ASP cc_start: 0.7357 (m-30) cc_final: 0.6847 (m-30) REVERT: I 822 MET cc_start: 0.8559 (mmm) cc_final: 0.7926 (mmt) REVERT: I 863 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7968 (ttm) REVERT: I 869 GLN cc_start: 0.8975 (mm110) cc_final: 0.8599 (mm110) REVERT: L 729 MET cc_start: 0.7459 (tpt) cc_final: 0.6889 (tpt) REVERT: L 746 MET cc_start: 0.6989 (tpp) cc_final: 0.6515 (tpt) REVERT: L 794 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8451 (tp-100) REVERT: L 869 GLN cc_start: 0.8882 (mm110) cc_final: 0.8509 (mm110) REVERT: Z 732 MET cc_start: 0.8295 (mtm) cc_final: 0.7944 (mtp) REVERT: Z 822 MET cc_start: 0.8205 (mmm) cc_final: 0.7976 (mmt) REVERT: Z 863 MET cc_start: 0.7957 (ttm) cc_final: 0.7608 (mtp) outliers start: 35 outliers final: 24 residues processed: 276 average time/residue: 0.1586 time to fit residues: 72.3355 Evaluate side-chains 272 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain I residue 863 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 274 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 794 GLN K 869 GLN Z 794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.103867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.083694 restraints weight = 28174.805| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 0.95 r_work: 0.2631 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 25296 Z= 0.351 Angle : 0.690 7.223 34242 Z= 0.341 Chirality : 0.049 0.162 3912 Planarity : 0.005 0.049 4338 Dihedral : 9.124 139.846 3480 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.23 % Allowed : 10.34 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3096 helix: 0.89 (0.13), residues: 1686 sheet: -1.32 (0.26), residues: 342 loop : -0.24 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 312 TYR 0.018 0.002 TYR B 143 PHE 0.013 0.002 PHE A 200 TRP 0.019 0.002 TRP E 340 HIS 0.007 0.002 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00880 (25296) covalent geometry : angle 0.68975 (34242) hydrogen bonds : bond 0.05680 ( 1300) hydrogen bonds : angle 4.79766 ( 3684) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.939 Fit side-chains REVERT: A 72 GLU cc_start: 0.8005 (tt0) cc_final: 0.7510 (mt-10) REVERT: A 118 LYS cc_start: 0.8302 (mttm) cc_final: 0.7735 (mmmt) REVERT: A 326 LYS cc_start: 0.8495 (tttp) cc_final: 0.8197 (tttm) REVERT: A 369 ILE cc_start: 0.8536 (tp) cc_final: 0.8241 (tp) REVERT: B 191 LYS cc_start: 0.8091 (tttp) cc_final: 0.7626 (tttt) REVERT: C 211 ASP cc_start: 0.8976 (t0) cc_final: 0.8696 (t70) REVERT: C 253 GLU cc_start: 0.8956 (mp0) cc_final: 0.8648 (mp0) REVERT: D 206 ARG cc_start: 0.7646 (ttm170) cc_final: 0.7292 (ttp-170) REVERT: E 47 MET cc_start: 0.7970 (mtp) cc_final: 0.7568 (mtt) REVERT: E 61 LYS cc_start: 0.8459 (mttm) cc_final: 0.8143 (mttm) REVERT: E 72 GLU cc_start: 0.8152 (tt0) cc_final: 0.7747 (tt0) REVERT: E 118 LYS cc_start: 0.8653 (mttm) cc_final: 0.8036 (mmmt) REVERT: E 354 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8017 (pt0) REVERT: F 57 GLU cc_start: 0.8470 (pt0) cc_final: 0.8198 (pt0) REVERT: F 61 LYS cc_start: 0.8578 (mttm) cc_final: 0.8105 (mtpp) REVERT: H 729 MET cc_start: 0.8441 (tpt) cc_final: 0.7738 (tpt) REVERT: I 732 MET cc_start: 0.8314 (mtp) cc_final: 0.8025 (mtp) REVERT: I 746 MET cc_start: 0.7923 (mmm) cc_final: 0.7626 (tpp) REVERT: I 822 MET cc_start: 0.8610 (mmm) cc_final: 0.8018 (mmt) REVERT: I 869 GLN cc_start: 0.8978 (mm110) cc_final: 0.8584 (mm110) REVERT: L 746 MET cc_start: 0.7169 (tpp) cc_final: 0.6761 (tpt) REVERT: Z 732 MET cc_start: 0.8318 (mtm) cc_final: 0.7924 (mtp) outliers start: 33 outliers final: 28 residues processed: 275 average time/residue: 0.1717 time to fit residues: 75.2725 Evaluate side-chains 276 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 235 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.107886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.087507 restraints weight = 27428.379| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.01 r_work: 0.2680 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25296 Z= 0.134 Angle : 0.530 7.275 34242 Z= 0.258 Chirality : 0.041 0.156 3912 Planarity : 0.003 0.038 4338 Dihedral : 8.874 143.956 3480 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.12 % Allowed : 10.90 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 3096 helix: 1.32 (0.13), residues: 1692 sheet: -1.33 (0.27), residues: 324 loop : -0.11 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 829 TYR 0.008 0.001 TYR B 143 PHE 0.009 0.001 PHE F 31 TRP 0.016 0.001 TRP C 340 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00313 (25296) covalent geometry : angle 0.53042 (34242) hydrogen bonds : bond 0.04431 ( 1300) hydrogen bonds : angle 4.44281 ( 3684) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.977 Fit side-chains REVERT: A 72 GLU cc_start: 0.8006 (tt0) cc_final: 0.7473 (mt-10) REVERT: A 118 LYS cc_start: 0.8342 (mttm) cc_final: 0.7802 (mmmt) REVERT: A 326 LYS cc_start: 0.8487 (tttp) cc_final: 0.8186 (tttm) REVERT: B 191 LYS cc_start: 0.7973 (tttp) cc_final: 0.7520 (tttt) REVERT: C 211 ASP cc_start: 0.8877 (t0) cc_final: 0.8519 (t0) REVERT: E 47 MET cc_start: 0.7760 (mtp) cc_final: 0.7425 (mtt) REVERT: E 72 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: E 354 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7976 (pt0) REVERT: F 57 GLU cc_start: 0.8468 (pt0) cc_final: 0.8182 (pt0) REVERT: H 729 MET cc_start: 0.8391 (tpt) cc_final: 0.7780 (tpt) REVERT: I 732 MET cc_start: 0.8211 (mtp) cc_final: 0.7940 (mtm) REVERT: I 822 MET cc_start: 0.8521 (mmm) cc_final: 0.7923 (mmt) REVERT: I 869 GLN cc_start: 0.8969 (mm110) cc_final: 0.8591 (mm110) REVERT: L 746 MET cc_start: 0.7023 (tpp) cc_final: 0.6595 (tpt) REVERT: Z 732 MET cc_start: 0.8305 (mtm) cc_final: 0.7729 (mtp) outliers start: 30 outliers final: 24 residues processed: 255 average time/residue: 0.1482 time to fit residues: 62.4616 Evaluate side-chains 259 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 794 GLN Z 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.109085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.088668 restraints weight = 27521.838| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 0.98 r_work: 0.2750 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25296 Z= 0.127 Angle : 0.511 6.668 34242 Z= 0.247 Chirality : 0.040 0.156 3912 Planarity : 0.003 0.035 4338 Dihedral : 8.592 147.253 3480 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.97 % Allowed : 11.09 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 3096 helix: 1.50 (0.13), residues: 1698 sheet: -1.21 (0.27), residues: 324 loop : 0.08 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 862 TYR 0.009 0.001 TYR F 143 PHE 0.007 0.001 PHE F 31 TRP 0.016 0.001 TRP C 340 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00298 (25296) covalent geometry : angle 0.51098 (34242) hydrogen bonds : bond 0.04150 ( 1300) hydrogen bonds : angle 4.28950 ( 3684) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8324 (mttm) cc_final: 0.7768 (mmmt) REVERT: A 191 LYS cc_start: 0.8134 (tttp) cc_final: 0.7532 (tttp) REVERT: A 326 LYS cc_start: 0.8472 (tttp) cc_final: 0.8179 (tttm) REVERT: B 191 LYS cc_start: 0.8038 (tttp) cc_final: 0.7496 (tttt) REVERT: C 211 ASP cc_start: 0.8836 (t0) cc_final: 0.8512 (t0) REVERT: D 206 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7245 (ttp-170) REVERT: E 47 MET cc_start: 0.7716 (mtp) cc_final: 0.7413 (mtt) REVERT: E 72 GLU cc_start: 0.7932 (tt0) cc_final: 0.7392 (tt0) REVERT: E 354 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7972 (pt0) REVERT: F 57 GLU cc_start: 0.8468 (pt0) cc_final: 0.8176 (pt0) REVERT: F 227 MET cc_start: 0.8269 (mmt) cc_final: 0.7615 (mmm) REVERT: F 344 SER cc_start: 0.8648 (m) cc_final: 0.8224 (p) REVERT: G 795 GLN cc_start: 0.9001 (mt0) cc_final: 0.8724 (mt0) REVERT: H 729 MET cc_start: 0.8386 (tpt) cc_final: 0.7790 (tpt) REVERT: H 794 GLN cc_start: 0.9055 (tp40) cc_final: 0.8714 (tp-100) REVERT: I 732 MET cc_start: 0.8208 (mtp) cc_final: 0.7952 (mtm) REVERT: I 805 ASP cc_start: 0.7328 (m-30) cc_final: 0.6786 (m-30) REVERT: I 822 MET cc_start: 0.8503 (mmm) cc_final: 0.7924 (mmt) REVERT: I 869 GLN cc_start: 0.8959 (mm110) cc_final: 0.8600 (mm110) REVERT: L 729 MET cc_start: 0.7231 (tpt) cc_final: 0.6889 (tpt) REVERT: L 746 MET cc_start: 0.6894 (tpp) cc_final: 0.6416 (tpt) REVERT: L 869 GLN cc_start: 0.8877 (mm110) cc_final: 0.8505 (mm110) REVERT: Z 732 MET cc_start: 0.8263 (mtm) cc_final: 0.7931 (mtm) REVERT: Z 822 MET cc_start: 0.8230 (mmm) cc_final: 0.8014 (mmt) outliers start: 26 outliers final: 23 residues processed: 261 average time/residue: 0.1629 time to fit residues: 69.5874 Evaluate side-chains 263 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 206 optimal weight: 2.9990 chunk 76 optimal weight: 0.0470 chunk 261 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 260 optimal weight: 0.6980 chunk 300 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 763 ASN I 763 ASN L 763 ASN L 794 GLN Z 794 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.110530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.090777 restraints weight = 27195.737| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.00 r_work: 0.2766 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25296 Z= 0.107 Angle : 0.497 7.393 34242 Z= 0.238 Chirality : 0.039 0.144 3912 Planarity : 0.003 0.035 4338 Dihedral : 8.379 155.795 3480 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.00 % Allowed : 11.42 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.16), residues: 3096 helix: 1.79 (0.13), residues: 1668 sheet: -0.81 (0.27), residues: 354 loop : 0.33 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 862 TYR 0.009 0.001 TYR E 143 PHE 0.007 0.001 PHE F 31 TRP 0.015 0.001 TRP C 340 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00242 (25296) covalent geometry : angle 0.49670 (34242) hydrogen bonds : bond 0.03885 ( 1300) hydrogen bonds : angle 4.17808 ( 3684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5109.31 seconds wall clock time: 88 minutes 45.78 seconds (5325.78 seconds total)