Starting phenix.real_space_refine on Sun Jul 5 01:41:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uuw_26805/07_2026/7uuw_26805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uuw_26805/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7uuw_26805/07_2026/7uuw_26805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uuw_26805/07_2026/7uuw_26805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uuw_26805/07_2026/7uuw_26805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uuw_26805/07_2026/7uuw_26805.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uuw_26805/07_2026/7uuw_26805.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uuw_26805/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.65, per 1000 atoms: 0.23 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: 2.48 Conformation dependent library (CDL) restraints added in 1.4 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: 0.76 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: 5.73 Time building geometry restraints manager: 3.24 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: 0.10 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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/Z covalent geometry : bond 0.00704 / 0.29 (25296) covalent geometry : angle 0.74983 / 0.39 (34242) hydrogen bonds : bond 0.15765 / 10.47 ( 1300) hydrogen bonds : angle 6.68532 / 4.78 ( 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 : 0.930 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: 0.7662 (mtp) REVERT: A 157 ASP cc_start: 0.8839 (t0) cc_final: 0.8518 (t70) REVERT: A 176 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: A 211 ASP cc_start: 0.8634 (t0) cc_final: 0.8249 (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: 0.6909 (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: 0.8264 (t0) REVERT: C 313 MET cc_start: 0.8000 (ttt) cc_final: 0.7739 (ttm) REVERT: D 119 MET cc_start: 0.8108 (mtm) cc_final: 0.7901 (mtm) REVERT: D 313 MET cc_start: 0.8358 (ttt) cc_final: 0.7942 (ttt) REVERT: D 325 MET cc_start: 0.8022 (mmt) cc_final: 0.7808 (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: 0.8072 (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: 0.7126 (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: 0.6797 (ptp) REVERT: H 725 MET cc_start: 0.7749 (mtt) cc_final: 0.7359 (mtt) REVERT: H 822 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8179 (mmp) REVERT: H 863 MET cc_start: 0.8121 (mtm) cc_final: 0.7619 (mtm) REVERT: I 732 MET cc_start: 0.8281 (mtp) cc_final: 0.8017 (mtp) REVERT: K 869 GLN cc_start: 0.8795 (mm110) cc_final: 0.8505 (mm-40) REVERT: L 732 MET cc_start: 0.8189 (mtp) cc_final: 0.7969 (mtm) REVERT: L 746 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7455 (tpt) REVERT: L 794 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8341 (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: 0.7560 (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: 0.7687 (mmm) REVERT: Z 863 MET cc_start: 0.7501 (mtm) cc_final: 0.7142 (mtm) outliers start: 36 outliers final: 7 residues processed: 335 average time/residue: 0.1644 time to fit residues: 88.9467 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 : 0.874 ------------------------------------------------------------------------------- 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... 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 = 0.3093 r_free = 0.3093 target = 0.110995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.091206 restraints weight = 27316.832| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 0.91 r_work: 0.2706 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25296 Z= 0.132 Angle : 0.555 7.729 34242 Z= 0.277 Chirality : 0.041 0.155 3912 Planarity : 0.004 0.037 4338 Dihedral : 12.039 170.489 3511 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 0.55 (0.16), residues: 3096 helix: 1.14 (0.13), residues: 1686 sheet: -1.28 (0.27), residues: 378 loop : -0.08 (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 0.014 0.001 TRP E 340 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (25296) covalent geometry : angle 0.55510 / 0.28 (34242) hydrogen bonds : bond 0.04858 / 3.19 ( 1300) hydrogen bonds : angle 4.89342 / 3.51 ( 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 303 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 0.981 Fit side-chains REVERT: A 118 LYS cc_start: 0.8227 (mttm) cc_final: 0.7702 (mmmt) REVERT: A 119 MET cc_start: 0.8198 (mtm) cc_final: 0.7889 (mtp) REVERT: A 157 ASP cc_start: 0.8930 (t0) cc_final: 0.8714 (t0) REVERT: B 66 THR cc_start: 0.9280 (p) cc_final: 0.9066 (p) REVERT: B 123 MET cc_start: 0.8778 (mmt) cc_final: 0.8487 (mmm) REVERT: B 191 LYS cc_start: 0.7859 (tttp) cc_final: 0.7539 (tttt) REVERT: B 205 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 313 MET cc_start: 0.8306 (ttt) cc_final: 0.7891 (ttt) REVERT: B 326 LYS cc_start: 0.8236 (ttpp) cc_final: 0.8017 (tttp) REVERT: C 82 MET cc_start: 0.8611 (tpt) cc_final: 0.8396 (tpt) REVERT: C 211 ASP cc_start: 0.8737 (t0) cc_final: 0.8437 (t0) REVERT: D 191 LYS cc_start: 0.7773 (tttp) cc_final: 0.7376 (tptt) REVERT: D 311 ASP cc_start: 0.8017 (m-30) cc_final: 0.7804 (m-30) REVERT: D 313 MET cc_start: 0.8544 (ttt) cc_final: 0.8150 (ttt) REVERT: E 72 GLU cc_start: 0.7829 (tt0) cc_final: 0.7471 (tt0) REVERT: E 354 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7834 (pt0) REVERT: E 355 MET cc_start: 0.9239 (mtt) cc_final: 0.9024 (mtm) REVERT: F 44 MET cc_start: 0.8521 (mtt) cc_final: 0.8280 (mtp) REVERT: F 57 GLU cc_start: 0.8547 (pt0) cc_final: 0.8090 (pt0) REVERT: F 283 MET cc_start: 0.8531 (mmm) cc_final: 0.8305 (mmt) REVERT: G 805 ASP cc_start: 0.6905 (m-30) cc_final: 0.6516 (m-30) REVERT: H 729 MET cc_start: 0.8406 (tpt) cc_final: 0.7624 (tpt) REVERT: H 822 MET cc_start: 0.8308 (mmm) cc_final: 0.8081 (mmm) REVERT: I 732 MET cc_start: 0.8324 (mtp) cc_final: 0.8057 (mtp) REVERT: I 822 MET cc_start: 0.8527 (mmm) cc_final: 0.7856 (mmt) REVERT: K 746 MET cc_start: 0.7895 (mmm) cc_final: 0.7399 (tpp) REVERT: L 729 MET cc_start: 0.7687 (tpt) cc_final: 0.7308 (tpt) REVERT: L 732 MET cc_start: 0.8290 (mtm) cc_final: 0.8032 (mtm) REVERT: L 746 MET cc_start: 0.7297 (tpp) cc_final: 0.6936 (tpt) REVERT: L 822 MET cc_start: 0.8492 (mmp) cc_final: 0.8228 (mmt) REVERT: Z 732 MET cc_start: 0.8338 (mtm) cc_final: 0.8000 (mtp) REVERT: Z 746 MET cc_start: 0.7710 (tpp) cc_final: 0.7501 (mmm) REVERT: Z 794 GLN cc_start: 0.9134 (tp40) cc_final: 0.8898 (tp40) REVERT: Z 863 MET cc_start: 0.7587 (mtm) cc_final: 0.7129 (mtm) outliers start: 22 outliers final: 17 residues processed: 292 average time/residue: 0.1588 time to fit residues: 76.4884 Evaluate side-chains 277 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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: 0.8980 chunk 192 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 297 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 252 ASN L 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 = 0.3032 r_free = 0.3032 target = 0.106510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.086327 restraints weight = 27949.761| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 0.97 r_work: 0.2669 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25296 Z= 0.195 Angle : 0.570 6.653 34242 Z= 0.281 Chirality : 0.043 0.155 3912 Planarity : 0.004 0.035 4338 Dihedral : 10.533 153.300 3486 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.15 % Allowed : 7.59 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 3096 helix: 1.16 (0.13), residues: 1686 sheet: -1.35 (0.27), residues: 366 loop : -0.10 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 256 TYR 0.012 0.001 TYR E 143 PHE 0.010 0.001 PHE C 255 TRP 0.017 0.002 TRP E 340 HIS 0.004 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.19 (25296) covalent geometry : angle 0.56974 / 0.28 (34242) hydrogen bonds : bond 0.05005 / 3.28 ( 1300) hydrogen bonds : angle 4.72784 / 3.39 ( 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 294 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 0.923 Fit side-chains REVERT: A 118 LYS cc_start: 0.8246 (mttm) cc_final: 0.7669 (mmmt) REVERT: A 119 MET cc_start: 0.7984 (mtm) cc_final: 0.7717 (mtp) REVERT: A 176 MET cc_start: 0.8620 (mmm) cc_final: 0.8369 (mmm) REVERT: A 364 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 176 MET cc_start: 0.8437 (mtt) cc_final: 0.8050 (mtt) REVERT: B 191 LYS cc_start: 0.7857 (tttp) cc_final: 0.7491 (tttt) REVERT: B 305 MET cc_start: 0.8997 (mtp) cc_final: 0.8763 (mmm) REVERT: B 326 LYS cc_start: 0.8329 (ttpp) cc_final: 0.7984 (tttp) REVERT: C 211 ASP cc_start: 0.8838 (t0) cc_final: 0.8500 (t0) REVERT: D 191 LYS cc_start: 0.7932 (tttp) cc_final: 0.7324 (ttmt) REVERT: D 311 ASP cc_start: 0.8063 (m-30) cc_final: 0.7830 (m-30) REVERT: D 313 MET cc_start: 0.8568 (ttt) cc_final: 0.8338 (ttt) REVERT: E 72 GLU cc_start: 0.7927 (tt0) cc_final: 0.7536 (tt0) REVERT: E 354 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7914 (pt0) REVERT: E 355 MET cc_start: 0.9194 (mtt) cc_final: 0.8990 (mtm) REVERT: F 57 GLU cc_start: 0.8620 (pt0) cc_final: 0.8179 (pt0) REVERT: F 61 LYS cc_start: 0.8540 (mttm) cc_final: 0.8264 (mttm) REVERT: F 325 MET cc_start: 0.8979 (mmp) cc_final: 0.8625 (mmp) REVERT: G 863 MET cc_start: 0.8486 (mtm) cc_final: 0.8041 (mtp) REVERT: H 729 MET cc_start: 0.8342 (tpt) cc_final: 0.7494 (tpt) REVERT: I 732 MET cc_start: 0.8347 (mtp) cc_final: 0.8119 (mtm) REVERT: I 822 MET cc_start: 0.8581 (mmm) cc_final: 0.8023 (mmt) REVERT: K 746 MET cc_start: 0.7706 (mmm) cc_final: 0.7225 (tpp) REVERT: L 746 MET cc_start: 0.7293 (tpp) cc_final: 0.6957 (tpt) REVERT: L 822 MET cc_start: 0.8462 (mmp) cc_final: 0.8235 (mmt) REVERT: Z 732 MET cc_start: 0.8306 (mtm) cc_final: 0.8029 (mtm) REVERT: Z 746 MET cc_start: 0.7652 (tpp) cc_final: 0.7436 (mmm) REVERT: Z 794 GLN cc_start: 0.9145 (tp40) cc_final: 0.8932 (tp40) REVERT: Z 863 MET cc_start: 0.7747 (mtm) cc_final: 0.7202 (mtm) outliers start: 31 outliers final: 28 residues processed: 283 average time/residue: 0.1582 time to fit residues: 74.1293 Evaluate side-chains 280 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 252 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 GLU 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 283 MET 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 167 GLU 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 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 229 THR 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 L residue 863 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 286 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 353 GLN K 794 GLN L 794 GLN L 837 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.108825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.088326 restraints weight = 27374.605| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 1.00 r_work: 0.2705 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1421 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= 0.119 Angle : 0.507 6.470 34242 Z= 0.248 Chirality : 0.040 0.143 3912 Planarity : 0.003 0.034 4338 Dihedral : 9.724 136.071 3480 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.86 % Allowed : 8.56 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 3096 helix: 1.39 (0.13), residues: 1692 sheet: -1.15 (0.28), residues: 330 loop : -0.07 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 829 TYR 0.010 0.001 TYR B 143 PHE 0.007 0.001 PHE F 31 TRP 0.013 0.001 TRP E 340 HIS 0.002 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (25296) covalent geometry : angle 0.50656 / 0.25 (34242) hydrogen bonds : bond 0.04309 / 2.83 ( 1300) hydrogen bonds : angle 4.47105 / 3.21 ( 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 284 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 1.004 Fit side-chains REVERT: A 72 GLU cc_start: 0.7866 (tt0) cc_final: 0.7286 (mt-10) REVERT: A 118 LYS cc_start: 0.8223 (mttm) cc_final: 0.7671 (mmmt) REVERT: A 119 MET cc_start: 0.7871 (mtm) cc_final: 0.7668 (mtp) REVERT: A 176 MET cc_start: 0.8679 (mmm) cc_final: 0.8463 (mmm) REVERT: A 354 GLN cc_start: 0.8563 (pt0) cc_final: 0.8334 (pt0) REVERT: A 364 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7448 (mt-10) REVERT: A 369 ILE cc_start: 0.8523 (tp) cc_final: 0.8269 (tp) REVERT: B 176 MET cc_start: 0.8322 (mtt) cc_final: 0.7976 (mtt) REVERT: B 191 LYS cc_start: 0.7873 (tttp) cc_final: 0.7445 (tttt) REVERT: B 205 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7966 (mt-10) REVERT: B 305 MET cc_start: 0.8952 (mtp) cc_final: 0.8717 (mmm) REVERT: B 326 LYS cc_start: 0.8343 (ttpp) cc_final: 0.8005 (tttp) REVERT: B 372 ARG cc_start: 0.8027 (mtm180) cc_final: 0.7634 (mtp180) REVERT: C 211 ASP cc_start: 0.8818 (t0) cc_final: 0.8503 (t0) REVERT: D 311 ASP cc_start: 0.8038 (m-30) cc_final: 0.7810 (m-30) REVERT: D 313 MET cc_start: 0.8567 (ttt) cc_final: 0.8353 (ttt) REVERT: E 72 GLU cc_start: 0.7892 (tt0) cc_final: 0.7311 (tt0) REVERT: E 354 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8011 (pt0) REVERT: F 57 GLU cc_start: 0.8651 (pt0) cc_final: 0.8237 (pt0) REVERT: F 125 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8048 (mt-10) REVERT: F 325 MET cc_start: 0.8965 (mmp) cc_final: 0.8750 (mmp) REVERT: G 795 GLN cc_start: 0.9003 (mt0) cc_final: 0.8744 (mt0) REVERT: G 863 MET cc_start: 0.8502 (mtm) cc_final: 0.8087 (mtp) REVERT: H 729 MET cc_start: 0.8323 (tpt) cc_final: 0.7510 (tpt) REVERT: I 732 MET cc_start: 0.8285 (mtp) cc_final: 0.7908 (mtp) REVERT: I 805 ASP cc_start: 0.7334 (m-30) cc_final: 0.6859 (m-30) REVERT: I 822 MET cc_start: 0.8514 (mmm) cc_final: 0.8081 (mmt) REVERT: I 863 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7776 (ttm) REVERT: I 869 GLN cc_start: 0.9140 (mm110) cc_final: 0.8713 (mm110) REVERT: K 746 MET cc_start: 0.7632 (mmm) cc_final: 0.7181 (tpp) REVERT: L 729 MET cc_start: 0.7414 (tpt) cc_final: 0.7102 (tpt) REVERT: L 732 MET cc_start: 0.8372 (mtp) cc_final: 0.8148 (mtm) REVERT: L 746 MET cc_start: 0.7165 (tpp) cc_final: 0.6805 (tpt) REVERT: Z 732 MET cc_start: 0.8310 (mtm) cc_final: 0.8093 (mtm) REVERT: Z 746 MET cc_start: 0.7530 (tpp) cc_final: 0.7317 (mmm) REVERT: Z 863 MET cc_start: 0.7788 (mtm) cc_final: 0.7203 (mtm) outliers start: 23 outliers final: 19 residues processed: 273 average time/residue: 0.1585 time to fit residues: 71.6525 Evaluate side-chains 270 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 350 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 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 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 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: 4.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 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: 2.9990 chunk 276 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 HIS E 360 GLN I 837 GLN K 794 GLN L 837 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.103846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.083836 restraints weight = 28078.446| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 0.94 r_work: 0.2630 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 25296 Z= 0.329 Angle : 0.683 7.233 34242 Z= 0.338 Chirality : 0.048 0.176 3912 Planarity : 0.004 0.044 4338 Dihedral : 9.677 136.886 3480 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 9.64 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3096 helix: 0.86 (0.13), residues: 1686 sheet: -1.38 (0.28), residues: 330 loop : -0.25 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 206 TYR 0.016 0.002 TYR D 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/Z covalent geometry : bond 0.00827 / 0.33 (25296) covalent geometry : angle 0.68302 / 0.34 (34242) hydrogen bonds : bond 0.05729 / 3.76 ( 1300) hydrogen bonds : angle 4.85938 / 3.49 ( 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 286 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.938 Fit side-chains REVERT: A 118 LYS cc_start: 0.8325 (mttm) cc_final: 0.7750 (mmmt) REVERT: A 326 LYS cc_start: 0.8535 (tttp) cc_final: 0.8209 (tttm) REVERT: A 354 GLN cc_start: 0.8641 (pt0) cc_final: 0.8411 (pt0) REVERT: A 364 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 369 ILE cc_start: 0.8557 (tp) cc_final: 0.8297 (tp) REVERT: B 191 LYS cc_start: 0.8084 (tttp) cc_final: 0.7718 (tttt) REVERT: B 305 MET cc_start: 0.9044 (mtp) cc_final: 0.8839 (mmm) REVERT: C 211 ASP cc_start: 0.8954 (t0) cc_final: 0.8689 (t70) REVERT: D 206 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7345 (ttp-170) REVERT: D 313 MET cc_start: 0.8644 (ttt) cc_final: 0.8208 (ttt) REVERT: D 372 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7870 (mtp180) REVERT: E 47 MET cc_start: 0.7688 (mtp) cc_final: 0.7468 (mtt) REVERT: E 72 GLU cc_start: 0.8174 (tt0) cc_final: 0.7745 (tt0) REVERT: E 118 LYS cc_start: 0.8660 (mttm) cc_final: 0.8050 (mmmt) REVERT: E 354 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7888 (pt0) REVERT: F 57 GLU cc_start: 0.8542 (pt0) cc_final: 0.8220 (pt0) REVERT: F 61 LYS cc_start: 0.8594 (mttm) cc_final: 0.8304 (mttm) REVERT: F 325 MET cc_start: 0.9024 (mmp) cc_final: 0.8823 (mmp) REVERT: G 863 MET cc_start: 0.8592 (mtm) cc_final: 0.8219 (mtp) REVERT: H 729 MET cc_start: 0.8442 (tpt) cc_final: 0.7661 (tpt) REVERT: I 690 ILE cc_start: 0.6692 (mt) cc_final: 0.6460 (mm) REVERT: I 732 MET cc_start: 0.8348 (mtp) cc_final: 0.8083 (mtp) REVERT: I 822 MET cc_start: 0.8659 (mmm) cc_final: 0.7990 (mmt) REVERT: I 863 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8385 (ttm) REVERT: L 746 MET cc_start: 0.7229 (tpp) cc_final: 0.6871 (tpt) REVERT: Z 732 MET cc_start: 0.8333 (mtm) cc_final: 0.8011 (mtm) outliers start: 34 outliers final: 27 residues processed: 276 average time/residue: 0.1665 time to fit residues: 73.1882 Evaluate side-chains 270 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 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 167 GLU 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 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: 0.5980 chunk 223 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 287 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 HIS L 794 GLN L 837 GLN Z 794 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.111139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.092198 restraints weight = 27222.405| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 0.86 r_work: 0.2744 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25296 Z= 0.120 Angle : 0.512 6.504 34242 Z= 0.251 Chirality : 0.040 0.148 3912 Planarity : 0.003 0.039 4338 Dihedral : 9.351 144.444 3480 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.15 % Allowed : 10.12 % Favored : 88.73 % 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: 0.77 (0.16), residues: 3096 helix: 1.34 (0.13), residues: 1692 sheet: -1.23 (0.27), residues: 330 loop : -0.08 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.009 0.001 TYR B 143 PHE 0.008 0.001 PHE D 255 TRP 0.015 0.001 TRP C 340 HIS 0.002 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (25296) covalent geometry : angle 0.51155 / 0.25 (34242) hydrogen bonds : bond 0.04319 / 2.85 ( 1300) hydrogen bonds : angle 4.44735 / 3.20 ( 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 278 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.966 Fit side-chains REVERT: A 82 MET cc_start: 0.8484 (tpt) cc_final: 0.8229 (tpt) REVERT: A 118 LYS cc_start: 0.8352 (mttm) cc_final: 0.7787 (mmmt) REVERT: A 326 LYS cc_start: 0.8521 (tttp) cc_final: 0.8203 (tttm) REVERT: A 354 GLN cc_start: 0.8608 (pt0) cc_final: 0.8379 (pt0) REVERT: A 364 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7698 (mm-30) REVERT: A 369 ILE cc_start: 0.8554 (tp) cc_final: 0.8256 (tp) REVERT: B 191 LYS cc_start: 0.7943 (tttp) cc_final: 0.7472 (tttt) REVERT: B 205 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7969 (mt-10) REVERT: B 305 MET cc_start: 0.8935 (mtp) cc_final: 0.8716 (mmm) REVERT: C 211 ASP cc_start: 0.8820 (t0) cc_final: 0.8491 (t0) REVERT: E 72 GLU cc_start: 0.8024 (tt0) cc_final: 0.7513 (tt0) REVERT: E 354 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8008 (pt0) REVERT: F 57 GLU cc_start: 0.8484 (pt0) cc_final: 0.8198 (pt0) REVERT: F 61 LYS cc_start: 0.8550 (mttm) cc_final: 0.8283 (mttm) REVERT: F 125 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8076 (mt-10) REVERT: G 863 MET cc_start: 0.8674 (mtm) cc_final: 0.8368 (mtp) REVERT: H 729 MET cc_start: 0.8464 (tpt) cc_final: 0.7780 (tpt) REVERT: I 732 MET cc_start: 0.8374 (mtp) cc_final: 0.8136 (mtm) REVERT: I 822 MET cc_start: 0.8601 (mmm) cc_final: 0.7947 (mmt) REVERT: I 863 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7892 (ttm) REVERT: I 869 GLN cc_start: 0.8977 (mm110) cc_final: 0.8587 (mm110) REVERT: L 729 MET cc_start: 0.7527 (tpt) cc_final: 0.6920 (tpt) REVERT: L 746 MET cc_start: 0.7149 (tpp) cc_final: 0.6761 (tpt) REVERT: L 869 GLN cc_start: 0.8886 (mm110) cc_final: 0.8521 (mm110) REVERT: Z 732 MET cc_start: 0.8415 (mtm) cc_final: 0.8123 (mtm) REVERT: Z 863 MET cc_start: 0.8193 (ttm) cc_final: 0.7830 (mtp) outliers start: 31 outliers final: 21 residues processed: 266 average time/residue: 0.1560 time to fit residues: 67.9867 Evaluate side-chains 264 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 57 GLU 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 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 206 ARG 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 863 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 134 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 133 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3034 r_free = 0.3034 target = 0.106698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.086703 restraints weight = 27722.303| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 0.94 r_work: 0.2670 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 25296 Z= 0.195 Angle : 0.561 6.473 34242 Z= 0.274 Chirality : 0.043 0.164 3912 Planarity : 0.004 0.036 4338 Dihedral : 9.222 142.412 3480 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.23 % Allowed : 10.79 % 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: 0.68 (0.15), residues: 3096 helix: 1.27 (0.13), residues: 1692 sheet: -1.31 (0.27), residues: 330 loop : -0.12 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.013 0.001 TYR D 143 PHE 0.009 0.001 PHE F 31 TRP 0.017 0.002 TRP E 340 HIS 0.004 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.19 (25296) covalent geometry : angle 0.56146 / 0.27 (34242) hydrogen bonds : bond 0.04715 / 3.10 ( 1300) hydrogen bonds : angle 4.51988 / 3.25 ( 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 288 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.982 Fit side-chains REVERT: A 72 GLU cc_start: 0.8012 (tt0) cc_final: 0.7531 (mt-10) REVERT: A 118 LYS cc_start: 0.8316 (mttm) cc_final: 0.7718 (mmmt) REVERT: A 326 LYS cc_start: 0.8486 (tttp) cc_final: 0.8171 (tttm) REVERT: A 354 GLN cc_start: 0.8621 (pt0) cc_final: 0.8387 (pt0) REVERT: A 364 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7668 (mm-30) REVERT: A 369 ILE cc_start: 0.8509 (tp) cc_final: 0.8214 (tp) REVERT: B 191 LYS cc_start: 0.8013 (tttp) cc_final: 0.7567 (tttt) REVERT: B 205 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8039 (mt-10) REVERT: B 305 MET cc_start: 0.8974 (mtp) cc_final: 0.8754 (mmm) REVERT: C 211 ASP cc_start: 0.8883 (t0) cc_final: 0.8539 (t0) REVERT: C 253 GLU cc_start: 0.9013 (mp0) cc_final: 0.8700 (mp0) REVERT: E 72 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: E 354 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7965 (pt0) REVERT: F 57 GLU cc_start: 0.8489 (pt0) cc_final: 0.8155 (pt0) REVERT: F 61 LYS cc_start: 0.8539 (mttm) cc_final: 0.8099 (mtpp) REVERT: F 125 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8073 (mt-10) REVERT: G 863 MET cc_start: 0.8678 (mtm) cc_final: 0.8340 (mtp) REVERT: H 729 MET cc_start: 0.8429 (tpt) cc_final: 0.7726 (tpt) REVERT: I 732 MET cc_start: 0.8311 (mtp) cc_final: 0.8032 (mtm) REVERT: I 822 MET cc_start: 0.8555 (mmm) cc_final: 0.7931 (mmt) REVERT: I 863 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8001 (ttm) REVERT: I 869 GLN cc_start: 0.8970 (mm110) cc_final: 0.8593 (mm110) REVERT: L 746 MET cc_start: 0.7077 (tpp) cc_final: 0.6665 (tpt) REVERT: L 869 GLN cc_start: 0.8874 (mm110) cc_final: 0.8508 (mm110) REVERT: Z 732 MET cc_start: 0.8346 (mtm) cc_final: 0.7951 (mtp) REVERT: Z 863 MET cc_start: 0.8195 (ttm) cc_final: 0.7784 (mtp) outliers start: 33 outliers final: 27 residues processed: 275 average time/residue: 0.1598 time to fit residues: 71.9342 Evaluate side-chains 280 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 167 GLU 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 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 167 GLU Chi-restraints excluded: chain D residue 176 MET 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 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 Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.107134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.087042 restraints weight = 27616.839| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 0.95 r_work: 0.2678 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25296 Z= 0.182 Angle : 0.551 7.407 34242 Z= 0.268 Chirality : 0.042 0.161 3912 Planarity : 0.003 0.036 4338 Dihedral : 9.033 143.304 3480 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.41 % Allowed : 10.90 % Favored : 87.69 % 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: 0.70 (0.15), residues: 3096 helix: 1.30 (0.13), residues: 1692 sheet: -1.33 (0.27), residues: 330 loop : -0.12 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 256 TYR 0.011 0.001 TYR D 143 PHE 0.009 0.001 PHE F 31 TRP 0.016 0.001 TRP E 340 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (25296) covalent geometry : angle 0.55105 / 0.27 (34242) hydrogen bonds : bond 0.04612 / 3.03 ( 1300) hydrogen bonds : angle 4.47960 / 3.22 ( 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: 38 poor density : 248 time to evaluate : 0.898 Fit side-chains REVERT: A 72 GLU cc_start: 0.7991 (tt0) cc_final: 0.7493 (mt-10) REVERT: A 118 LYS cc_start: 0.8372 (mttm) cc_final: 0.7830 (mmmt) REVERT: A 326 LYS cc_start: 0.8496 (tttp) cc_final: 0.8195 (tttm) REVERT: A 354 GLN cc_start: 0.8636 (pt0) cc_final: 0.8404 (pt0) REVERT: A 364 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7667 (mm-30) REVERT: A 369 ILE cc_start: 0.8508 (tp) cc_final: 0.8193 (tp) REVERT: B 191 LYS cc_start: 0.8013 (tttp) cc_final: 0.7441 (tttt) REVERT: B 205 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8034 (mt-10) REVERT: B 305 MET cc_start: 0.8957 (mtp) cc_final: 0.8740 (mmm) REVERT: C 211 ASP cc_start: 0.8868 (t0) cc_final: 0.8552 (t0) REVERT: D 206 ARG cc_start: 0.7594 (ttm170) cc_final: 0.7271 (ttp-170) REVERT: E 72 GLU cc_start: 0.8119 (tt0) cc_final: 0.7593 (tt0) REVERT: E 118 LYS cc_start: 0.8602 (mttm) cc_final: 0.8010 (mmmt) REVERT: E 354 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7974 (pt0) REVERT: F 57 GLU cc_start: 0.8477 (pt0) cc_final: 0.8179 (pt0) REVERT: F 125 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8070 (mt-10) REVERT: G 863 MET cc_start: 0.8697 (mtm) cc_final: 0.8367 (mtm) REVERT: H 729 MET cc_start: 0.8475 (tpt) cc_final: 0.7828 (tpt) REVERT: I 732 MET cc_start: 0.8346 (mtp) cc_final: 0.8068 (mtm) REVERT: I 805 ASP cc_start: 0.7426 (m-30) cc_final: 0.6904 (m-30) REVERT: I 863 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7952 (ttm) REVERT: I 869 GLN cc_start: 0.8973 (mm110) cc_final: 0.8598 (mm110) REVERT: L 746 MET cc_start: 0.7068 (tpp) cc_final: 0.6648 (tpt) REVERT: L 869 GLN cc_start: 0.8904 (mm110) cc_final: 0.8533 (mm110) REVERT: Z 732 MET cc_start: 0.8353 (mtm) cc_final: 0.7997 (mtp) REVERT: Z 863 MET cc_start: 0.8194 (ttm) cc_final: 0.7858 (mtp) outliers start: 38 outliers final: 30 residues processed: 274 average time/residue: 0.1556 time to fit residues: 69.3934 Evaluate side-chains 276 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 B residue 34 ILE Chi-restraints excluded: chain B residue 57 GLU 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 167 GLU 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 232 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 327 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain I residue 863 MET 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: 4.9990 chunk 229 optimal weight: 7.9990 chunk 310 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 208 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 40 HIS K 794 GLN L 794 GLN Z 794 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.109712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.089473 restraints weight = 27265.126| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 0.98 r_work: 0.2759 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25296 Z= 0.114 Angle : 0.500 6.584 34242 Z= 0.241 Chirality : 0.040 0.153 3912 Planarity : 0.003 0.035 4338 Dihedral : 8.707 145.791 3480 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.19 % Allowed : 11.16 % Favored : 87.65 % 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: 1.22 (0.16), residues: 3096 helix: 1.71 (0.13), residues: 1656 sheet: -0.92 (0.27), residues: 360 loop : 0.16 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 335 TYR 0.009 0.001 TYR D 143 PHE 0.007 0.001 PHE F 31 TRP 0.015 0.001 TRP E 340 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (25296) covalent geometry : angle 0.49955 / 0.24 (34242) hydrogen bonds : bond 0.04031 / 2.65 ( 1300) hydrogen bonds : angle 4.26276 / 3.06 ( 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 278 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8372 (mttm) cc_final: 0.7752 (mmmt) REVERT: A 191 LYS cc_start: 0.8065 (tttp) cc_final: 0.7437 (tttp) REVERT: A 326 LYS cc_start: 0.8465 (tttp) cc_final: 0.8083 (tttm) REVERT: A 354 GLN cc_start: 0.8611 (pt0) cc_final: 0.8379 (pt0) REVERT: A 364 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7629 (mm-30) REVERT: B 191 LYS cc_start: 0.8010 (tttp) cc_final: 0.7480 (tttt) REVERT: B 205 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 305 MET cc_start: 0.8922 (mtp) cc_final: 0.8688 (mmm) REVERT: C 145 SER cc_start: 0.9197 (t) cc_final: 0.8846 (m) REVERT: C 211 ASP cc_start: 0.8822 (t0) cc_final: 0.8473 (t0) REVERT: E 72 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: E 354 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7934 (pt0) REVERT: F 57 GLU cc_start: 0.8455 (pt0) cc_final: 0.8164 (pt0) REVERT: F 227 MET cc_start: 0.8219 (mmt) cc_final: 0.7494 (mmm) REVERT: G 795 GLN cc_start: 0.8979 (mt0) cc_final: 0.8700 (mt0) REVERT: G 863 MET cc_start: 0.8691 (mtm) cc_final: 0.8439 (mtm) REVERT: H 729 MET cc_start: 0.8393 (tpt) cc_final: 0.7783 (tpt) REVERT: H 794 GLN cc_start: 0.9057 (tp40) cc_final: 0.8714 (tp-100) REVERT: I 725 MET cc_start: 0.7810 (mtt) cc_final: 0.7150 (mtt) REVERT: I 732 MET cc_start: 0.8166 (mtp) cc_final: 0.7886 (mtm) REVERT: I 805 ASP cc_start: 0.7307 (m-30) cc_final: 0.6775 (m-30) REVERT: I 822 MET cc_start: 0.8479 (mmm) cc_final: 0.7867 (mmt) REVERT: I 863 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7801 (ttm) REVERT: I 869 GLN cc_start: 0.8953 (mm110) cc_final: 0.8598 (mm110) REVERT: L 729 MET cc_start: 0.7315 (tpt) cc_final: 0.6992 (tpt) REVERT: L 746 MET cc_start: 0.6876 (tpp) cc_final: 0.6391 (tpt) REVERT: L 869 GLN cc_start: 0.8876 (mm110) cc_final: 0.8510 (mm110) REVERT: Z 732 MET cc_start: 0.8262 (mtm) cc_final: 0.7642 (mtp) REVERT: Z 822 MET cc_start: 0.8217 (mmm) cc_final: 0.7997 (mmt) outliers start: 32 outliers final: 26 residues processed: 269 average time/residue: 0.1569 time to fit residues: 69.1440 Evaluate side-chains 269 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 57 GLU 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 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 232 SER 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 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 327 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 863 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 294 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.108647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.088569 restraints weight = 27626.108| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 0.94 r_work: 0.2703 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25296 Z= 0.142 Angle : 0.521 6.812 34242 Z= 0.251 Chirality : 0.041 0.155 3912 Planarity : 0.003 0.034 4338 Dihedral : 8.616 146.942 3480 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.08 % Allowed : 11.50 % Favored : 87.43 % 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: 1.06 (0.16), residues: 3096 helix: 1.52 (0.13), residues: 1698 sheet: -0.93 (0.27), residues: 360 loop : 0.09 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 335 TYR 0.011 0.001 TYR D 143 PHE 0.008 0.001 PHE F 31 TRP 0.017 0.001 TRP E 340 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (25296) covalent geometry : angle 0.52145 / 0.25 (34242) hydrogen bonds : bond 0.04206 / 2.77 ( 1300) hydrogen bonds : angle 4.29770 / 3.09 ( 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: 29 poor density : 240 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8019 (tt0) cc_final: 0.7499 (mt-10) REVERT: A 118 LYS cc_start: 0.8403 (mttm) cc_final: 0.7807 (mmmt) REVERT: A 326 LYS cc_start: 0.8465 (tttp) cc_final: 0.8178 (tttm) REVERT: A 354 GLN cc_start: 0.8605 (pt0) cc_final: 0.8383 (pt0) REVERT: A 364 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7649 (mm-30) REVERT: B 191 LYS cc_start: 0.8050 (tttp) cc_final: 0.7511 (tttt) REVERT: B 205 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 305 MET cc_start: 0.8926 (mtp) cc_final: 0.8701 (mmm) REVERT: C 211 ASP cc_start: 0.8835 (t0) cc_final: 0.8504 (t0) REVERT: E 72 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: E 354 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7987 (pt0) REVERT: F 57 GLU cc_start: 0.8492 (pt0) cc_final: 0.8216 (pt0) REVERT: G 730 MET cc_start: 0.7783 (tpt) cc_final: 0.7467 (tpt) REVERT: G 795 GLN cc_start: 0.9014 (mt0) cc_final: 0.8735 (mt0) REVERT: G 805 ASP cc_start: 0.6844 (m-30) cc_final: 0.6448 (m-30) REVERT: G 863 MET cc_start: 0.8644 (mtm) cc_final: 0.8414 (mtm) REVERT: H 729 MET cc_start: 0.8440 (tpt) cc_final: 0.7845 (tpt) REVERT: I 732 MET cc_start: 0.8253 (mtp) cc_final: 0.7988 (mtm) REVERT: I 805 ASP cc_start: 0.7356 (m-30) cc_final: 0.6833 (m-30) REVERT: I 822 MET cc_start: 0.8525 (mmm) cc_final: 0.7924 (mmt) REVERT: I 863 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7941 (ttm) REVERT: I 869 GLN cc_start: 0.8974 (mm110) cc_final: 0.8599 (mm110) REVERT: L 729 MET cc_start: 0.7405 (tpt) cc_final: 0.7071 (tpt) REVERT: L 746 MET cc_start: 0.6899 (tpp) cc_final: 0.6415 (tpt) REVERT: L 869 GLN cc_start: 0.8882 (mm110) cc_final: 0.8519 (mm110) REVERT: Z 732 MET cc_start: 0.8277 (mtm) cc_final: 0.7892 (mtp) REVERT: Z 822 MET cc_start: 0.8230 (mmm) cc_final: 0.8021 (mmt) outliers start: 29 outliers final: 25 residues processed: 262 average time/residue: 0.1589 time to fit residues: 68.4022 Evaluate side-chains 265 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 B residue 57 GLU 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 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 232 SER 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 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 327 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 863 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 206 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 260 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 197 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3075 r_free = 0.3075 target = 0.109878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.089885 restraints weight = 27234.357| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 0.93 r_work: 0.2767 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25296 Z= 0.116 Angle : 0.500 6.857 34242 Z= 0.240 Chirality : 0.040 0.157 3912 Planarity : 0.003 0.034 4338 Dihedral : 8.470 150.956 3480 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.08 % Allowed : 11.57 % Favored : 87.35 % 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: 1.34 (0.16), residues: 3096 helix: 1.78 (0.13), residues: 1662 sheet: -0.82 (0.27), residues: 360 loop : 0.24 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 862 TYR 0.010 0.001 TYR D 143 PHE 0.008 0.001 PHE Z 697 TRP 0.015 0.001 TRP E 340 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (25296) covalent geometry : angle 0.49984 / 0.24 (34242) hydrogen bonds : bond 0.03990 / 2.63 ( 1300) hydrogen bonds : angle 4.21283 / 3.03 ( 3684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5302.81 seconds wall clock time: 92 minutes 2.54 seconds (5522.54 seconds total)