Starting phenix.real_space_refine on Sat Jun 21 11:52:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uuw_26805/06_2025/7uuw_26805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uuw_26805/06_2025/7uuw_26805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uuw_26805/06_2025/7uuw_26805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uuw_26805/06_2025/7uuw_26805.map" model { file = "/net/cci-nas-00/data/ceres_data/7uuw_26805/06_2025/7uuw_26805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uuw_26805/06_2025/7uuw_26805.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 22.56, per 1000 atoms: 0.91 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: 8.90 Conformation dependent library (CDL) restraints added in 3.8 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: 3.20 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: 18.93 Time building geometry restraints manager: 9.93 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: 0.21 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 153.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.220 Set scattering table: 0.310 Process input model: 86.750 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:4.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 25296 Z= 0.293 Angle : 0.750 13.916 34242 Z= 0.392 Chirality : 0.046 0.171 3912 Planarity : 0.004 0.040 4338 Dihedral : 17.000 172.062 9480 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.34 % Allowed : 3.53 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP A 340 HIS 0.003 0.001 HIS C 87 PHE 0.013 0.001 PHE Z 697 TYR 0.014 0.002 TYR D 279 ARG 0.004 0.001 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.15765 ( 1300) hydrogen bonds : angle 6.68532 ( 3684) covalent geometry : bond 0.00704 (25296) covalent geometry : angle 0.74983 (34242) *********************** 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 : 3.827 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: 0.8479 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: A 211 ASP cc_start: 0.8633 (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: 0.7840 (ttt) REVERT: B 349 LEU cc_start: 0.8477 (mt) cc_final: 0.8178 (mt) REVERT: C 82 MET cc_start: 0.8551 (tpt) cc_final: 0.8341 (tpt) REVERT: C 211 ASP cc_start: 0.8594 (t0) cc_final: 0.8265 (t0) REVERT: C 313 MET cc_start: 0.8000 (ttt) cc_final: 0.7739 (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: 0.8023 (mmt) cc_final: 0.7808 (mmt) REVERT: E 100 GLU cc_start: 0.7838 (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: 0.7333 (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: 0.7497 (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: 0.7561 (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: 0.4357 time to fit residues: 237.6819 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 : 3.433 ------------------------------------------------------------------------------- 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 263 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 283 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 353 GLN K 794 GLN L 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.108229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.088656 restraints weight = 27386.731| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 0.97 r_work: 0.2740 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 25296 Z= 0.125 Angle : 0.553 7.903 34242 Z= 0.277 Chirality : 0.041 0.156 3912 Planarity : 0.004 0.037 4338 Dihedral : 12.235 173.185 3511 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.71 % Allowed : 5.84 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 3096 helix: 1.12 (0.13), residues: 1686 sheet: -1.27 (0.27), residues: 378 loop : -0.09 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 340 HIS 0.006 0.001 HIS C 40 PHE 0.007 0.001 PHE B 127 TYR 0.011 0.001 TYR F 143 ARG 0.005 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 1300) hydrogen bonds : angle 4.95251 ( 3684) covalent geometry : bond 0.00272 (25296) covalent geometry : angle 0.55308 (34242) *********************** 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 300 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 281 time to evaluate : 2.848 Fit side-chains REVERT: A 118 LYS cc_start: 0.8196 (mttm) cc_final: 0.7646 (mmmt) REVERT: A 119 MET cc_start: 0.8207 (mtm) cc_final: 0.7906 (mtp) REVERT: A 157 ASP cc_start: 0.8929 (t0) cc_final: 0.8720 (t0) REVERT: B 66 THR cc_start: 0.9276 (p) cc_final: 0.9063 (p) REVERT: B 123 MET cc_start: 0.8733 (mmt) cc_final: 0.8428 (mmm) REVERT: B 191 LYS cc_start: 0.7849 (tttp) cc_final: 0.7534 (tttt) REVERT: B 205 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7760 (mt-10) REVERT: B 313 MET cc_start: 0.8294 (ttt) cc_final: 0.7867 (ttt) REVERT: B 326 LYS cc_start: 0.8259 (ttpp) cc_final: 0.8011 (tttp) REVERT: B 349 LEU cc_start: 0.8556 (mt) cc_final: 0.8309 (mt) REVERT: C 82 MET cc_start: 0.8583 (tpt) cc_final: 0.8358 (tpt) REVERT: C 211 ASP cc_start: 0.8725 (t0) cc_final: 0.8417 (t0) REVERT: D 191 LYS cc_start: 0.7746 (tttp) cc_final: 0.7338 (tptt) REVERT: D 311 ASP cc_start: 0.8021 (m-30) cc_final: 0.7808 (m-30) REVERT: D 313 MET cc_start: 0.8531 (ttt) cc_final: 0.8137 (ttt) REVERT: D 355 MET cc_start: 0.9158 (mtt) cc_final: 0.8943 (mtt) REVERT: E 355 MET cc_start: 0.9230 (mtt) cc_final: 0.8984 (mtm) REVERT: F 44 MET cc_start: 0.8483 (mtt) cc_final: 0.8262 (mtp) REVERT: F 57 GLU cc_start: 0.8582 (pt0) cc_final: 0.8146 (pt0) REVERT: F 283 MET cc_start: 0.8514 (mmm) cc_final: 0.8262 (mmt) REVERT: G 746 MET cc_start: 0.7256 (tpp) cc_final: 0.6927 (mmm) REVERT: H 729 MET cc_start: 0.8384 (tpt) cc_final: 0.7597 (tpt) REVERT: H 822 MET cc_start: 0.8278 (mmm) cc_final: 0.7952 (mmp) REVERT: I 732 MET cc_start: 0.8224 (mtp) cc_final: 0.7938 (mtp) REVERT: I 822 MET cc_start: 0.8500 (mmm) cc_final: 0.7778 (mmt) REVERT: K 746 MET cc_start: 0.7891 (mmm) cc_final: 0.7367 (tpp) REVERT: K 869 GLN cc_start: 0.8807 (mm110) cc_final: 0.8528 (mm-40) REVERT: L 729 MET cc_start: 0.7643 (tpt) cc_final: 0.7282 (tpt) REVERT: L 732 MET cc_start: 0.8265 (mtm) cc_final: 0.8010 (mtm) REVERT: L 746 MET cc_start: 0.7511 (tpp) cc_final: 0.6989 (tpt) REVERT: Z 732 MET cc_start: 0.8329 (mtm) cc_final: 0.7810 (mtp) REVERT: Z 794 GLN cc_start: 0.9168 (tp40) cc_final: 0.8911 (tp40) REVERT: Z 863 MET cc_start: 0.7492 (mtm) cc_final: 0.7078 (mtm) outliers start: 19 outliers final: 17 residues processed: 290 average time/residue: 0.3282 time to fit residues: 156.7578 Evaluate side-chains 278 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET 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 176 MET 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 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 47 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 153 optimal weight: 0.0770 chunk 233 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 303 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 301 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 353 GLN I 837 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 = 0.3058 r_free = 0.3058 target = 0.108587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.088752 restraints weight = 27431.683| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 0.92 r_work: 0.2706 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25296 Z= 0.134 Angle : 0.523 6.397 34242 Z= 0.257 Chirality : 0.041 0.156 3912 Planarity : 0.003 0.035 4338 Dihedral : 10.459 149.982 3492 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.00 % Allowed : 7.22 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 3096 helix: 1.32 (0.13), residues: 1698 sheet: -1.15 (0.29), residues: 330 loop : -0.06 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 340 HIS 0.003 0.001 HIS C 40 PHE 0.009 0.001 PHE B 127 TYR 0.011 0.001 TYR E 143 ARG 0.003 0.000 ARG D 256 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 1300) hydrogen bonds : angle 4.55471 ( 3684) covalent geometry : bond 0.00313 (25296) covalent geometry : angle 0.52346 (34242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 2.984 Fit side-chains REVERT: A 72 GLU cc_start: 0.8052 (tt0) cc_final: 0.7384 (mt-10) REVERT: A 118 LYS cc_start: 0.8235 (mttm) cc_final: 0.7644 (mmmt) REVERT: A 119 MET cc_start: 0.7944 (mtm) cc_final: 0.7607 (mtp) REVERT: A 157 ASP cc_start: 0.8922 (t0) cc_final: 0.8692 (t0) REVERT: A 364 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7545 (mt-10) REVERT: A 369 ILE cc_start: 0.8498 (tp) cc_final: 0.8223 (tp) REVERT: B 66 THR cc_start: 0.9313 (p) cc_final: 0.9083 (p) REVERT: B 176 MET cc_start: 0.8339 (mtt) cc_final: 0.7953 (mtt) REVERT: B 191 LYS cc_start: 0.7832 (tttp) cc_final: 0.7526 (tttt) REVERT: B 205 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7698 (mt-10) REVERT: B 326 LYS cc_start: 0.8351 (ttpp) cc_final: 0.8035 (tttp) REVERT: C 82 MET cc_start: 0.8551 (tpt) cc_final: 0.8326 (tpt) REVERT: C 211 ASP cc_start: 0.8766 (t0) cc_final: 0.8469 (t0) REVERT: D 191 LYS cc_start: 0.7857 (tttp) cc_final: 0.7173 (tttt) REVERT: D 311 ASP cc_start: 0.8031 (m-30) cc_final: 0.7817 (m-30) REVERT: D 313 MET cc_start: 0.8529 (ttt) cc_final: 0.8306 (ttt) REVERT: D 354 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8140 (mm-40) REVERT: E 72 GLU cc_start: 0.7897 (tt0) cc_final: 0.7315 (tt0) REVERT: E 354 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7890 (pt0) REVERT: E 355 MET cc_start: 0.9162 (mtt) cc_final: 0.8949 (mtm) REVERT: F 57 GLU cc_start: 0.8616 (pt0) cc_final: 0.8178 (pt0) REVERT: F 325 MET cc_start: 0.8920 (mmp) cc_final: 0.8561 (mmp) REVERT: F 344 SER cc_start: 0.8588 (m) cc_final: 0.8275 (p) REVERT: G 746 MET cc_start: 0.7107 (tpp) cc_final: 0.6700 (mmm) REVERT: G 795 GLN cc_start: 0.9003 (mt0) cc_final: 0.8756 (mt0) REVERT: G 805 ASP cc_start: 0.6897 (m-30) cc_final: 0.6392 (m-30) REVERT: G 863 MET cc_start: 0.8425 (mtm) cc_final: 0.7951 (mtp) REVERT: H 729 MET cc_start: 0.8272 (tpt) cc_final: 0.7627 (tpt) REVERT: H 822 MET cc_start: 0.8297 (mmm) cc_final: 0.8090 (mmp) REVERT: I 732 MET cc_start: 0.8307 (mtp) cc_final: 0.7986 (mtp) REVERT: I 805 ASP cc_start: 0.7307 (m-30) cc_final: 0.6890 (m-30) REVERT: I 822 MET cc_start: 0.8546 (mmm) cc_final: 0.7991 (mmt) REVERT: K 746 MET cc_start: 0.7632 (mmm) cc_final: 0.7153 (tpp) REVERT: L 725 MET cc_start: 0.6989 (mtt) cc_final: 0.6764 (mtt) REVERT: L 746 MET cc_start: 0.7262 (tpp) cc_final: 0.6861 (tpt) REVERT: L 822 MET cc_start: 0.8422 (mmp) cc_final: 0.8187 (mmt) REVERT: Z 732 MET cc_start: 0.8311 (mtm) cc_final: 0.8063 (mtm) REVERT: Z 746 MET cc_start: 0.7313 (mmm) cc_final: 0.7079 (mmm) REVERT: Z 794 GLN cc_start: 0.9133 (tp40) cc_final: 0.8926 (tp40) REVERT: Z 863 MET cc_start: 0.7660 (mtm) cc_final: 0.7122 (mtm) outliers start: 27 outliers final: 22 residues processed: 286 average time/residue: 0.3674 time to fit residues: 172.8805 Evaluate side-chains 275 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 4.098 ------------------------------------------------------------------------------- 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 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 300 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 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 230 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 288 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS I 837 GLN K 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 = 0.3055 r_free = 0.3055 target = 0.108294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.088109 restraints weight = 27639.679| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 0.95 r_work: 0.2698 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 25296 Z= 0.150 Angle : 0.527 6.774 34242 Z= 0.257 Chirality : 0.041 0.147 3912 Planarity : 0.003 0.033 4338 Dihedral : 9.457 128.799 3480 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.97 % Allowed : 8.41 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.16), residues: 3096 helix: 1.37 (0.13), residues: 1698 sheet: -1.11 (0.28), residues: 330 loop : 0.01 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 340 HIS 0.003 0.001 HIS E 88 PHE 0.008 0.001 PHE C 255 TYR 0.011 0.001 TYR B 143 ARG 0.002 0.000 ARG D 256 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 1300) hydrogen bonds : angle 4.47011 ( 3684) covalent geometry : bond 0.00358 (25296) covalent geometry : angle 0.52664 (34242) *********************** 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 294 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 3.031 Fit side-chains REVERT: A 72 GLU cc_start: 0.7921 (tt0) cc_final: 0.7324 (mt-10) REVERT: A 118 LYS cc_start: 0.8269 (mttm) cc_final: 0.7713 (mmmt) REVERT: A 157 ASP cc_start: 0.8916 (t0) cc_final: 0.8663 (t0) REVERT: A 176 MET cc_start: 0.8680 (mmm) cc_final: 0.8419 (mmm) REVERT: A 369 ILE cc_start: 0.8545 (tp) cc_final: 0.8235 (tp) REVERT: B 176 MET cc_start: 0.8327 (mtt) cc_final: 0.8006 (mtt) REVERT: B 191 LYS cc_start: 0.7841 (tttp) cc_final: 0.7495 (tttt) REVERT: B 372 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7630 (mtp180) REVERT: C 82 MET cc_start: 0.8511 (tpt) cc_final: 0.8300 (tpt) REVERT: C 211 ASP cc_start: 0.8829 (t0) cc_final: 0.8518 (t0) REVERT: D 311 ASP cc_start: 0.8038 (m-30) cc_final: 0.7822 (m-30) REVERT: D 313 MET cc_start: 0.8565 (ttt) cc_final: 0.8324 (ttt) REVERT: E 72 GLU cc_start: 0.7816 (tt0) cc_final: 0.7282 (tt0) REVERT: E 354 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8035 (pt0) REVERT: F 57 GLU cc_start: 0.8645 (pt0) cc_final: 0.8201 (pt0) REVERT: F 61 LYS cc_start: 0.8526 (mttm) cc_final: 0.8261 (mttm) REVERT: F 323 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8850 (p) REVERT: F 325 MET cc_start: 0.8978 (mmp) cc_final: 0.8712 (mmp) REVERT: G 746 MET cc_start: 0.6977 (tpp) cc_final: 0.6692 (mmm) REVERT: G 863 MET cc_start: 0.8484 (mtm) cc_final: 0.8050 (mtp) REVERT: H 729 MET cc_start: 0.8305 (tpt) cc_final: 0.7501 (tpt) REVERT: I 732 MET cc_start: 0.8291 (mtp) cc_final: 0.7890 (mtp) REVERT: I 805 ASP cc_start: 0.7320 (m-30) cc_final: 0.6843 (m-30) REVERT: I 822 MET cc_start: 0.8517 (mmm) cc_final: 0.8103 (mmt) REVERT: I 863 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8033 (ttm) REVERT: I 869 GLN cc_start: 0.9149 (mm110) cc_final: 0.8710 (mm110) REVERT: K 746 MET cc_start: 0.7620 (mmm) cc_final: 0.7170 (tpp) REVERT: L 729 MET cc_start: 0.7571 (tpt) cc_final: 0.7219 (tpt) REVERT: L 746 MET cc_start: 0.7174 (tpp) cc_final: 0.6746 (tpt) REVERT: Z 732 MET cc_start: 0.8294 (mtm) cc_final: 0.7930 (mtp) REVERT: Z 863 MET cc_start: 0.7814 (mtm) cc_final: 0.7223 (mtm) outliers start: 26 outliers final: 21 residues processed: 283 average time/residue: 0.3392 time to fit residues: 157.8174 Evaluate side-chains 275 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 2.655 ------------------------------------------------------------------------------- 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 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain I residue 863 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 162 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 233 optimal weight: 0.0970 chunk 291 optimal weight: 2.9990 chunk 236 optimal weight: 0.0370 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 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 = 0.3073 r_free = 0.3073 target = 0.109898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.089869 restraints weight = 27423.672| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 0.97 r_work: 0.2763 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1617 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= 0.112 Angle : 0.491 6.362 34242 Z= 0.238 Chirality : 0.040 0.148 3912 Planarity : 0.003 0.033 4338 Dihedral : 9.213 138.143 3480 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.04 % Allowed : 8.71 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 3096 helix: 1.70 (0.13), residues: 1662 sheet: -0.84 (0.28), residues: 360 loop : 0.28 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 340 HIS 0.002 0.001 HIS E 88 PHE 0.007 0.001 PHE C 255 TYR 0.009 0.001 TYR B 143 ARG 0.002 0.000 ARG F 116 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 1300) hydrogen bonds : angle 4.30421 ( 3684) covalent geometry : bond 0.00254 (25296) covalent geometry : angle 0.49104 (34242) *********************** 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 287 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 2.954 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8264 (mttm) cc_final: 0.7730 (mmmt) REVERT: A 157 ASP cc_start: 0.8924 (t0) cc_final: 0.8668 (t0) REVERT: A 176 MET cc_start: 0.8704 (mmm) cc_final: 0.8453 (mmm) REVERT: A 369 ILE cc_start: 0.8489 (tp) cc_final: 0.8160 (tp) REVERT: B 66 THR cc_start: 0.9317 (p) cc_final: 0.9063 (p) REVERT: B 118 LYS cc_start: 0.8330 (mttm) cc_final: 0.7655 (mmmt) REVERT: B 191 LYS cc_start: 0.7885 (tttp) cc_final: 0.7549 (tttt) REVERT: B 305 MET cc_start: 0.8928 (mtp) cc_final: 0.8678 (mmm) REVERT: B 372 ARG cc_start: 0.8028 (mtm180) cc_final: 0.7636 (mtp180) REVERT: C 145 SER cc_start: 0.9173 (t) cc_final: 0.8860 (m) REVERT: C 211 ASP cc_start: 0.8807 (t0) cc_final: 0.8503 (t0) REVERT: D 313 MET cc_start: 0.8538 (ttt) cc_final: 0.8303 (ttt) REVERT: E 72 GLU cc_start: 0.7781 (tt0) cc_final: 0.7220 (tt0) REVERT: E 354 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7968 (pt0) REVERT: F 57 GLU cc_start: 0.8597 (pt0) cc_final: 0.8175 (pt0) REVERT: F 344 SER cc_start: 0.8505 (m) cc_final: 0.8231 (p) REVERT: G 746 MET cc_start: 0.6836 (tpp) cc_final: 0.6518 (mmm) REVERT: G 795 GLN cc_start: 0.8966 (mt0) cc_final: 0.8666 (mt0) REVERT: G 805 ASP cc_start: 0.7634 (t0) cc_final: 0.6841 (m-30) REVERT: G 863 MET cc_start: 0.8526 (mtm) cc_final: 0.8133 (mtp) REVERT: H 729 MET cc_start: 0.8314 (tpt) cc_final: 0.7798 (tpt) REVERT: H 794 GLN cc_start: 0.9015 (tp40) cc_final: 0.8717 (tp-100) REVERT: I 732 MET cc_start: 0.8154 (mtp) cc_final: 0.7726 (mtp) REVERT: I 805 ASP cc_start: 0.7267 (m-30) cc_final: 0.6797 (m-30) REVERT: I 822 MET cc_start: 0.8561 (mmm) cc_final: 0.8236 (mmt) REVERT: I 863 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7909 (ttm) REVERT: I 869 GLN cc_start: 0.9137 (mm110) cc_final: 0.8729 (mm110) REVERT: K 746 MET cc_start: 0.7517 (mmm) cc_final: 0.7102 (tpp) REVERT: L 729 MET cc_start: 0.7486 (tpt) cc_final: 0.7032 (tpt) REVERT: L 746 MET cc_start: 0.7021 (tpp) cc_final: 0.6555 (tpt) REVERT: L 869 GLN cc_start: 0.8829 (mm110) cc_final: 0.8430 (mm110) REVERT: Z 732 MET cc_start: 0.8214 (mtm) cc_final: 0.7862 (mtp) REVERT: Z 794 GLN cc_start: 0.8886 (tp40) cc_final: 0.8686 (tp40) REVERT: Z 863 MET cc_start: 0.7785 (mtm) cc_final: 0.7163 (mtm) outliers start: 28 outliers final: 21 residues processed: 277 average time/residue: 0.3444 time to fit residues: 156.6560 Evaluate side-chains 276 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 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 276 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 270 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 chunk 258 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 16 optimal weight: 0.0040 chunk 30 optimal weight: 1.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 HIS L 794 GLN L 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.111990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.091912 restraints weight = 27061.965| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 0.97 r_work: 0.2750 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25296 Z= 0.093 Angle : 0.471 6.310 34242 Z= 0.226 Chirality : 0.039 0.154 3912 Planarity : 0.003 0.033 4338 Dihedral : 8.728 141.074 3480 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.89 % Allowed : 9.26 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.16), residues: 3096 helix: 1.93 (0.13), residues: 1656 sheet: -0.90 (0.26), residues: 396 loop : 0.50 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.002 0.001 HIS C 40 PHE 0.006 0.001 PHE B 127 TYR 0.008 0.001 TYR E 143 ARG 0.002 0.000 ARG K 829 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 1300) hydrogen bonds : angle 4.14616 ( 3684) covalent geometry : bond 0.00199 (25296) covalent geometry : angle 0.47142 (34242) *********************** 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 288 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 2.590 Fit side-chains REVERT: A 118 LYS cc_start: 0.8355 (mttm) cc_final: 0.7777 (mmmt) REVERT: A 176 MET cc_start: 0.8709 (mmm) cc_final: 0.8480 (mmm) REVERT: A 369 ILE cc_start: 0.8504 (tp) cc_final: 0.8144 (tp) REVERT: B 66 THR cc_start: 0.9300 (p) cc_final: 0.9063 (p) REVERT: B 118 LYS cc_start: 0.8325 (mttm) cc_final: 0.7657 (mmmt) REVERT: B 191 LYS cc_start: 0.7895 (tttp) cc_final: 0.7612 (tttt) REVERT: B 205 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 372 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7705 (mtp180) REVERT: C 61 LYS cc_start: 0.8512 (mttm) cc_final: 0.8277 (mtpt) REVERT: C 145 SER cc_start: 0.9134 (t) cc_final: 0.8868 (m) REVERT: C 211 ASP cc_start: 0.8783 (t0) cc_final: 0.8476 (t0) REVERT: E 72 GLU cc_start: 0.7846 (tt0) cc_final: 0.7262 (tt0) REVERT: E 327 ILE cc_start: 0.8298 (mm) cc_final: 0.7983 (mm) REVERT: E 354 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7879 (pt0) REVERT: F 57 GLU cc_start: 0.8601 (pt0) cc_final: 0.8244 (pt0) REVERT: F 299 MET cc_start: 0.9043 (mtm) cc_final: 0.8786 (mtm) REVERT: G 746 MET cc_start: 0.6759 (tpp) cc_final: 0.6493 (mmm) REVERT: G 795 GLN cc_start: 0.8901 (mt0) cc_final: 0.8700 (mt0) REVERT: G 805 ASP cc_start: 0.7625 (t0) cc_final: 0.6841 (m-30) REVERT: G 863 MET cc_start: 0.8477 (mtm) cc_final: 0.8152 (mtp) REVERT: H 729 MET cc_start: 0.8333 (tpt) cc_final: 0.7860 (tpt) REVERT: H 794 GLN cc_start: 0.9014 (tp40) cc_final: 0.8703 (tp-100) REVERT: I 732 MET cc_start: 0.8089 (mtp) cc_final: 0.7870 (mtm) REVERT: I 805 ASP cc_start: 0.7231 (m-30) cc_final: 0.6787 (m-30) REVERT: I 822 MET cc_start: 0.8542 (mmm) cc_final: 0.8235 (mmt) REVERT: I 869 GLN cc_start: 0.9144 (mm110) cc_final: 0.8747 (mm110) REVERT: K 746 MET cc_start: 0.7432 (mmm) cc_final: 0.7047 (tpp) REVERT: L 729 MET cc_start: 0.7359 (tpt) cc_final: 0.6945 (tpt) REVERT: L 746 MET cc_start: 0.6942 (tpp) cc_final: 0.6461 (tpt) REVERT: L 795 GLN cc_start: 0.8505 (mt0) cc_final: 0.8223 (mt0) REVERT: L 869 GLN cc_start: 0.8838 (mm110) cc_final: 0.8449 (mm110) REVERT: Z 732 MET cc_start: 0.8193 (mtp) cc_final: 0.7883 (mtp) outliers start: 24 outliers final: 19 residues processed: 279 average time/residue: 0.3268 time to fit residues: 150.5910 Evaluate side-chains 274 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 255 time to evaluate : 3.021 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 123 optimal weight: 0.6980 chunk 210 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 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 = 0.3076 r_free = 0.3076 target = 0.109856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.089673 restraints weight = 27439.060| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 0.95 r_work: 0.2764 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1813 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 : 0.502 6.451 34242 Z= 0.241 Chirality : 0.040 0.188 3912 Planarity : 0.003 0.030 4338 Dihedral : 8.568 142.312 3480 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.97 % Allowed : 9.82 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 3096 helix: 1.82 (0.13), residues: 1668 sheet: -0.72 (0.27), residues: 360 loop : 0.47 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 340 HIS 0.003 0.001 HIS E 88 PHE 0.007 0.001 PHE C 31 TYR 0.010 0.001 TYR B 143 ARG 0.002 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 1300) hydrogen bonds : angle 4.20998 ( 3684) covalent geometry : bond 0.00313 (25296) covalent geometry : angle 0.50166 (34242) *********************** 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 287 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 2.605 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8125 (tt0) cc_final: 0.7768 (mt-10) REVERT: A 118 LYS cc_start: 0.8340 (mttm) cc_final: 0.7759 (mmmt) REVERT: A 176 MET cc_start: 0.8787 (mmm) cc_final: 0.8568 (mmm) REVERT: A 364 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7842 (mt-10) REVERT: A 369 ILE cc_start: 0.8488 (tp) cc_final: 0.8132 (tp) REVERT: B 66 THR cc_start: 0.9311 (p) cc_final: 0.9049 (p) REVERT: B 118 LYS cc_start: 0.8323 (mttm) cc_final: 0.7663 (mmmt) REVERT: B 191 LYS cc_start: 0.7952 (tttp) cc_final: 0.7558 (tttt) REVERT: B 305 MET cc_start: 0.8915 (mtp) cc_final: 0.8678 (mmm) REVERT: B 372 ARG cc_start: 0.8057 (mtm180) cc_final: 0.7697 (mtp180) REVERT: C 145 SER cc_start: 0.9177 (t) cc_final: 0.8870 (m) REVERT: C 211 ASP cc_start: 0.8797 (t0) cc_final: 0.8493 (t0) REVERT: C 253 GLU cc_start: 0.8923 (mp0) cc_final: 0.8582 (mp0) REVERT: E 72 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: E 354 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7924 (pt0) REVERT: F 57 GLU cc_start: 0.8627 (pt0) cc_final: 0.8213 (pt0) REVERT: F 61 LYS cc_start: 0.8441 (mttm) cc_final: 0.8064 (mtpp) REVERT: G 746 MET cc_start: 0.6791 (tpp) cc_final: 0.6499 (mmm) REVERT: G 863 MET cc_start: 0.8599 (mtm) cc_final: 0.8282 (mtp) REVERT: H 729 MET cc_start: 0.8304 (tpt) cc_final: 0.7846 (tpt) REVERT: I 725 MET cc_start: 0.8185 (mmm) cc_final: 0.7889 (mtt) REVERT: I 732 MET cc_start: 0.8144 (mtp) cc_final: 0.7864 (mtm) REVERT: I 805 ASP cc_start: 0.7161 (m-30) cc_final: 0.6683 (m-30) REVERT: I 822 MET cc_start: 0.8531 (mmm) cc_final: 0.7882 (mmt) REVERT: I 869 GLN cc_start: 0.9149 (mm110) cc_final: 0.8740 (mm110) REVERT: K 725 MET cc_start: 0.8040 (mmm) cc_final: 0.7589 (mmm) REVERT: L 729 MET cc_start: 0.7368 (tpt) cc_final: 0.6909 (tpt) REVERT: L 746 MET cc_start: 0.6918 (tpp) cc_final: 0.6412 (tpt) REVERT: L 869 GLN cc_start: 0.8811 (mm110) cc_final: 0.8424 (mm110) REVERT: Z 732 MET cc_start: 0.8217 (mtp) cc_final: 0.7868 (mtp) REVERT: Z 822 MET cc_start: 0.8110 (mmm) cc_final: 0.7849 (mmt) outliers start: 26 outliers final: 21 residues processed: 277 average time/residue: 0.3288 time to fit residues: 149.4030 Evaluate side-chains 270 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 2.531 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 242 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS K 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.107799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.087823 restraints weight = 27703.660| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 0.95 r_work: 0.2691 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25296 Z= 0.179 Angle : 0.541 6.661 34242 Z= 0.263 Chirality : 0.042 0.146 3912 Planarity : 0.003 0.031 4338 Dihedral : 8.542 144.892 3480 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.04 % Allowed : 10.12 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 3096 helix: 1.69 (0.13), residues: 1662 sheet: -0.84 (0.27), residues: 360 loop : 0.31 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 340 HIS 0.004 0.001 HIS D 87 PHE 0.008 0.001 PHE D 255 TYR 0.011 0.001 TYR F 143 ARG 0.002 0.000 ARG E 290 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 1300) hydrogen bonds : angle 4.33105 ( 3684) covalent geometry : bond 0.00441 (25296) covalent geometry : angle 0.54113 (34242) *********************** 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 283 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 2.732 Fit side-chains REVERT: A 72 GLU cc_start: 0.8198 (tt0) cc_final: 0.7699 (mt-10) REVERT: A 118 LYS cc_start: 0.8359 (mttm) cc_final: 0.7794 (mmmt) REVERT: A 176 MET cc_start: 0.8811 (mmm) cc_final: 0.8604 (mmm) REVERT: A 326 LYS cc_start: 0.8481 (tttp) cc_final: 0.8197 (tttm) REVERT: A 364 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7886 (mt-10) REVERT: A 369 ILE cc_start: 0.8492 (tp) cc_final: 0.8137 (tp) REVERT: B 118 LYS cc_start: 0.8366 (mttm) cc_final: 0.7726 (mmmt) REVERT: B 191 LYS cc_start: 0.8015 (tttp) cc_final: 0.7605 (tttt) REVERT: B 305 MET cc_start: 0.8952 (mtp) cc_final: 0.8723 (mmm) REVERT: B 355 MET cc_start: 0.9293 (mtp) cc_final: 0.9067 (mtm) REVERT: B 372 ARG cc_start: 0.8112 (mtm180) cc_final: 0.7799 (mtp180) REVERT: C 211 ASP cc_start: 0.8855 (t0) cc_final: 0.8565 (t0) REVERT: E 72 GLU cc_start: 0.8119 (tt0) cc_final: 0.7580 (tt0) REVERT: E 354 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7905 (pt0) REVERT: F 57 GLU cc_start: 0.8532 (pt0) cc_final: 0.8202 (pt0) REVERT: F 61 LYS cc_start: 0.8463 (mttm) cc_final: 0.8071 (mtpp) REVERT: G 746 MET cc_start: 0.6834 (tpp) cc_final: 0.6502 (mmm) REVERT: G 805 ASP cc_start: 0.7762 (t0) cc_final: 0.6734 (m-30) REVERT: G 863 MET cc_start: 0.8692 (mtm) cc_final: 0.8242 (mtm) REVERT: H 729 MET cc_start: 0.8365 (tpt) cc_final: 0.7743 (tpt) REVERT: I 732 MET cc_start: 0.8197 (mtp) cc_final: 0.7930 (mtm) REVERT: I 805 ASP cc_start: 0.7297 (m-30) cc_final: 0.6807 (m-30) REVERT: I 822 MET cc_start: 0.8562 (mmm) cc_final: 0.7930 (mmt) REVERT: I 869 GLN cc_start: 0.8967 (mm110) cc_final: 0.8564 (mm110) REVERT: K 725 MET cc_start: 0.8039 (mmm) cc_final: 0.7450 (mmm) REVERT: L 729 MET cc_start: 0.7532 (tpt) cc_final: 0.7007 (tpt) REVERT: L 746 MET cc_start: 0.6981 (tpp) cc_final: 0.6481 (tpt) REVERT: L 869 GLN cc_start: 0.8902 (mm110) cc_final: 0.8509 (mm110) REVERT: Z 732 MET cc_start: 0.8269 (mtp) cc_final: 0.7910 (mtp) REVERT: Z 822 MET cc_start: 0.8130 (mmm) cc_final: 0.7874 (mmt) REVERT: Z 863 MET cc_start: 0.8161 (ttm) cc_final: 0.7886 (mtp) outliers start: 28 outliers final: 23 residues processed: 273 average time/residue: 0.3449 time to fit residues: 153.1913 Evaluate side-chains 274 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 2.647 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 297 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.108742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.088851 restraints weight = 27512.568| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 0.94 r_work: 0.2750 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25296 Z= 0.145 Angle : 0.515 6.550 34242 Z= 0.249 Chirality : 0.041 0.153 3912 Planarity : 0.003 0.031 4338 Dihedral : 8.450 147.951 3480 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.04 % Allowed : 10.38 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 3096 helix: 1.76 (0.13), residues: 1662 sheet: -0.83 (0.27), residues: 360 loop : 0.33 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 340 HIS 0.003 0.001 HIS E 88 PHE 0.008 0.001 PHE F 31 TYR 0.010 0.001 TYR D 143 ARG 0.002 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 1300) hydrogen bonds : angle 4.26616 ( 3684) covalent geometry : bond 0.00347 (25296) covalent geometry : angle 0.51526 (34242) *********************** 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 277 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 2.804 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8018 (tt0) cc_final: 0.7503 (mt-10) REVERT: A 118 LYS cc_start: 0.8348 (mttm) cc_final: 0.7775 (mmmt) REVERT: A 326 LYS cc_start: 0.8460 (tttp) cc_final: 0.8121 (tttm) REVERT: A 364 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7873 (mt-10) REVERT: A 369 ILE cc_start: 0.8498 (tp) cc_final: 0.8147 (tp) REVERT: B 118 LYS cc_start: 0.8352 (mttm) cc_final: 0.7704 (mmmt) REVERT: B 191 LYS cc_start: 0.7982 (tttp) cc_final: 0.7575 (tttt) REVERT: B 305 MET cc_start: 0.8927 (mtp) cc_final: 0.8700 (mmm) REVERT: B 355 MET cc_start: 0.9298 (mtp) cc_final: 0.9078 (mtm) REVERT: B 372 ARG cc_start: 0.8099 (mtm180) cc_final: 0.7797 (mtp180) REVERT: C 211 ASP cc_start: 0.8826 (t0) cc_final: 0.8523 (t0) REVERT: E 72 GLU cc_start: 0.7930 (tt0) cc_final: 0.7369 (tt0) REVERT: E 354 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7896 (pt0) REVERT: F 57 GLU cc_start: 0.8505 (pt0) cc_final: 0.8171 (pt0) REVERT: F 61 LYS cc_start: 0.8457 (mttm) cc_final: 0.8072 (mtpp) REVERT: G 746 MET cc_start: 0.6841 (tpp) cc_final: 0.6520 (mmm) REVERT: G 805 ASP cc_start: 0.7753 (t0) cc_final: 0.6699 (m-30) REVERT: G 863 MET cc_start: 0.8704 (mtm) cc_final: 0.8348 (mtm) REVERT: H 729 MET cc_start: 0.8358 (tpt) cc_final: 0.7745 (tpt) REVERT: I 732 MET cc_start: 0.8231 (mtp) cc_final: 0.7964 (mtm) REVERT: I 805 ASP cc_start: 0.7272 (m-30) cc_final: 0.6776 (m-30) REVERT: I 822 MET cc_start: 0.8552 (mmm) cc_final: 0.7931 (mmt) REVERT: I 869 GLN cc_start: 0.8958 (mm110) cc_final: 0.8559 (mm110) REVERT: L 729 MET cc_start: 0.7525 (tpt) cc_final: 0.6991 (tpt) REVERT: L 730 MET cc_start: 0.7113 (mtp) cc_final: 0.6808 (mtt) REVERT: L 746 MET cc_start: 0.6936 (tpp) cc_final: 0.6423 (tpt) REVERT: L 869 GLN cc_start: 0.8834 (mm110) cc_final: 0.8447 (mm110) REVERT: Z 732 MET cc_start: 0.8260 (mtp) cc_final: 0.7900 (mtp) REVERT: Z 822 MET cc_start: 0.8108 (mmm) cc_final: 0.7848 (mmt) REVERT: Z 863 MET cc_start: 0.8128 (ttm) cc_final: 0.7842 (mtp) outliers start: 28 outliers final: 24 residues processed: 266 average time/residue: 0.3425 time to fit residues: 148.6126 Evaluate side-chains 270 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 2.635 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 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 L residue 718 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 73 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 794 GLN L 794 GLN Z 794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.111304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.091178 restraints weight = 27279.623| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 0.96 r_work: 0.2741 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25296 Z= 0.101 Angle : 0.482 6.218 34242 Z= 0.232 Chirality : 0.039 0.142 3912 Planarity : 0.003 0.032 4338 Dihedral : 8.256 153.802 3480 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.97 % Allowed : 10.57 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.16), residues: 3096 helix: 1.95 (0.13), residues: 1668 sheet: -0.73 (0.27), residues: 354 loop : 0.46 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.002 0.001 HIS C 40 PHE 0.006 0.001 PHE F 31 TYR 0.008 0.001 TYR D 143 ARG 0.001 0.000 ARG K 829 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1300) hydrogen bonds : angle 4.11658 ( 3684) covalent geometry : bond 0.00222 (25296) covalent geometry : angle 0.48243 (34242) ********************** 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 278 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 2.903 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8359 (mttm) cc_final: 0.7781 (mmmt) REVERT: A 191 LYS cc_start: 0.8095 (tttp) cc_final: 0.7530 (tttp) REVERT: A 364 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7911 (mt-10) REVERT: B 66 THR cc_start: 0.9308 (p) cc_final: 0.9059 (p) REVERT: B 118 LYS cc_start: 0.8343 (mttm) cc_final: 0.7675 (mmmt) REVERT: B 191 LYS cc_start: 0.7914 (tttp) cc_final: 0.7520 (tttt) REVERT: B 205 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8022 (mt-10) REVERT: B 305 MET cc_start: 0.8891 (mtp) cc_final: 0.8653 (mmm) REVERT: B 372 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7760 (mtp180) REVERT: C 61 LYS cc_start: 0.8511 (mttm) cc_final: 0.8280 (mtpt) REVERT: C 145 SER cc_start: 0.9172 (t) cc_final: 0.8849 (m) REVERT: C 211 ASP cc_start: 0.8792 (t0) cc_final: 0.8442 (t0) REVERT: E 72 GLU cc_start: 0.7880 (tt0) cc_final: 0.7337 (tt0) REVERT: E 354 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7886 (pt0) REVERT: F 57 GLU cc_start: 0.8503 (pt0) cc_final: 0.8175 (pt0) REVERT: F 61 LYS cc_start: 0.8437 (mttm) cc_final: 0.8069 (mtpp) REVERT: F 227 MET cc_start: 0.8218 (mmt) cc_final: 0.7552 (mmm) REVERT: G 746 MET cc_start: 0.6731 (tpp) cc_final: 0.6453 (mmm) REVERT: G 805 ASP cc_start: 0.7704 (t0) cc_final: 0.6616 (m-30) REVERT: G 863 MET cc_start: 0.8645 (mtm) cc_final: 0.8363 (mtm) REVERT: H 729 MET cc_start: 0.8350 (tpt) cc_final: 0.7941 (tpt) REVERT: H 794 GLN cc_start: 0.9006 (tp40) cc_final: 0.8670 (tp40) REVERT: I 725 MET cc_start: 0.7981 (mtt) cc_final: 0.7019 (mtt) REVERT: I 732 MET cc_start: 0.8174 (mtp) cc_final: 0.7914 (mtm) REVERT: I 805 ASP cc_start: 0.7260 (m-30) cc_final: 0.6989 (m-30) REVERT: I 822 MET cc_start: 0.8621 (mmm) cc_final: 0.7896 (mmt) REVERT: I 869 GLN cc_start: 0.8955 (mm110) cc_final: 0.8567 (mm110) REVERT: L 729 MET cc_start: 0.7369 (tpt) cc_final: 0.6954 (tpt) REVERT: L 746 MET cc_start: 0.6823 (tpp) cc_final: 0.6324 (tpt) REVERT: L 869 GLN cc_start: 0.8843 (mm110) cc_final: 0.8457 (mm110) REVERT: Z 732 MET cc_start: 0.8220 (mtp) cc_final: 0.7875 (mtp) REVERT: Z 794 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8126 (tp-100) REVERT: Z 822 MET cc_start: 0.8076 (mmm) cc_final: 0.7826 (mmt) REVERT: Z 863 MET cc_start: 0.8100 (ttm) cc_final: 0.7900 (mtp) outliers start: 26 outliers final: 21 residues processed: 268 average time/residue: 0.3485 time to fit residues: 153.2393 Evaluate side-chains 269 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain Z residue 794 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 180 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.0010 chunk 215 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 290 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.111157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.090528 restraints weight = 27279.097| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 0.99 r_work: 0.2735 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 25296 Z= 0.120 Angle : 0.637 59.197 34242 Z= 0.345 Chirality : 0.042 0.911 3912 Planarity : 0.003 0.032 4338 Dihedral : 8.256 153.821 3480 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.82 % Allowed : 10.90 % Favored : 88.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 3096 helix: 1.95 (0.13), residues: 1668 sheet: -0.73 (0.27), residues: 354 loop : 0.47 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.002 0.001 HIS C 40 PHE 0.006 0.001 PHE F 31 TYR 0.008 0.001 TYR D 143 ARG 0.001 0.000 ARG K 829 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 1300) hydrogen bonds : angle 4.11615 ( 3684) covalent geometry : bond 0.00261 (25296) covalent geometry : angle 0.63709 (34242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11842.27 seconds wall clock time: 207 minutes 38.00 seconds (12458.00 seconds total)