Starting phenix.real_space_refine on Sat Mar 16 12:57:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8p_28932/03_2024/8f8p_28932_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8p_28932/03_2024/8f8p_28932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8p_28932/03_2024/8f8p_28932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8p_28932/03_2024/8f8p_28932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8p_28932/03_2024/8f8p_28932_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8p_28932/03_2024/8f8p_28932_updated.pdb" } resolution = 2.26 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= 0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 24": "OD1" <-> "OD2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 24": "OD1" <-> "OD2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 24": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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} Time building chain proxies: 7.94, per 1000 atoms: 0.54 Number of scatterers: 14640 At special positions: 0 Unit cell: (77.76, 99.36, 195.48, 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 105 16.00 P 10 15.00 Mg 5 11.99 O 2815 8.00 N 2470 7.00 C 9235 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 - 3.50 Amino acid : False - 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: 5.47 Conformation dependent library (CDL) restraints added in 2.7 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 20 sheets defined 42.6% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.020A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.839A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.865A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.955A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.784A pdb=" N SER A 338 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 369 through 373 removed outlier: 4.405A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 195 removed outlier: 4.019A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.839A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.866A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.955A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 347 removed outlier: 3.784A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 369 through 373 removed outlier: 4.404A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.020A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.838A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.866A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.955A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 347 removed outlier: 3.785A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 369 through 373 removed outlier: 4.405A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.019A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.838A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.865A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.954A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 347 removed outlier: 3.784A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 373 removed outlier: 4.405A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.020A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.840A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.865A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.956A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 347 removed outlier: 3.785A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 369 through 373 removed outlier: 4.405A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.718A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.238A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.718A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.238A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.718A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.238A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.718A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.238A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.718A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.238A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 520 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 5.94 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: 4717 1.34 - 1.46: 3198 1.46 - 1.58: 6845 1.58 - 1.70: 15 1.70 - 1.82: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.36e+00 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 99.80 - 107.09: 614 107.09 - 114.38: 8535 114.38 - 121.67: 7645 121.67 - 128.96: 3411 128.96 - 136.25: 100 Bond angle restraints: 20305 Sorted by residual: angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY E 46 " pdb=" N MET E 47 " pdb=" CA MET E 47 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.69e+01 ... (remaining 20300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 8610 35.73 - 71.46: 355 71.46 - 107.19: 20 107.19 - 142.92: 5 142.92 - 178.65: 5 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 121.35 178.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 121.36 178.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 121.37 178.63 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1287 0.033 - 0.065: 594 0.065 - 0.098: 214 0.098 - 0.131: 135 0.131 - 0.163: 25 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA CYS E 257 " pdb=" N CYS E 257 " pdb=" C CYS E 257 " pdb=" CB CYS E 257 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CB ILE E 309 " pdb=" CA ILE E 309 " pdb=" CG1 ILE E 309 " pdb=" CG2 ILE E 309 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO D 243 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 243 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 243 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.027 5.00e-02 4.00e+02 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4224 2.82 - 3.34: 11882 3.34 - 3.86: 24732 3.86 - 4.38: 29480 4.38 - 4.90: 50392 Nonbonded interactions: 120710 Sorted by model distance: nonbonded pdb=" O GLN A 314 " pdb=" OG1 THR A 318 " model vdw 2.301 2.440 nonbonded pdb=" O GLN D 314 " pdb=" OG1 THR D 318 " model vdw 2.301 2.440 nonbonded pdb=" O GLN E 314 " pdb=" OG1 THR E 318 " model vdw 2.301 2.440 nonbonded pdb=" O GLN C 314 " pdb=" OG1 THR C 318 " model vdw 2.302 2.440 nonbonded pdb=" O GLN B 314 " pdb=" OG1 THR B 318 " model vdw 2.302 2.440 ... (remaining 120705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.860 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: 0.010 Extract box with map and model: 4.220 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 40.840 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.004 0.055 14960 Z= 0.265 Angle : 0.825 10.502 20305 Z= 0.421 Chirality : 0.049 0.163 2255 Planarity : 0.006 0.049 2595 Dihedral : 17.731 178.653 5565 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.04 % Allowed : 22.81 % Favored : 75.14 % 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: -1.31 (0.19), residues: 1830 helix: -1.96 (0.14), residues: 745 sheet: 1.04 (0.30), residues: 345 loop : -0.37 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 356 HIS 0.003 0.001 HIS A 161 PHE 0.015 0.001 PHE B 255 TYR 0.010 0.001 TYR C 143 ARG 0.006 0.001 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 374 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8356 (m110) cc_final: 0.8152 (m-40) REVERT: A 115 ASN cc_start: 0.8126 (t0) cc_final: 0.7919 (t0) REVERT: A 252 ASN cc_start: 0.8441 (p0) cc_final: 0.8238 (p0) REVERT: B 225 ASN cc_start: 0.7838 (m-40) cc_final: 0.7575 (m-40) REVERT: B 283 MET cc_start: 0.8490 (mmm) cc_final: 0.8254 (mmt) REVERT: D 227 MET cc_start: 0.8628 (mmm) cc_final: 0.8342 (mmm) REVERT: D 288 ASP cc_start: 0.7881 (m-30) cc_final: 0.7665 (m-30) REVERT: D 299 MET cc_start: 0.8900 (mtm) cc_final: 0.8592 (mtm) outliers start: 32 outliers final: 11 residues processed: 391 average time/residue: 1.5113 time to fit residues: 637.7168 Evaluate side-chains 310 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 299 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 77 optimal weight: 0.0470 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 49 GLN A 59 GLN A 78 ASN A 162 ASN B 12 ASN B 59 GLN B 78 ASN B 115 ASN B 128 ASN B 297 ASN D 78 ASN D 162 ASN D 353 GLN E 173 HIS E 280 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14960 Z= 0.230 Angle : 0.579 6.178 20305 Z= 0.282 Chirality : 0.046 0.153 2255 Planarity : 0.005 0.037 2595 Dihedral : 9.256 146.416 2098 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.45 % Allowed : 20.32 % Favored : 76.23 % 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: -0.20 (0.19), residues: 1830 helix: -0.62 (0.18), residues: 745 sheet: 0.96 (0.28), residues: 350 loop : 0.08 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.005 0.001 HIS E 371 PHE 0.015 0.002 PHE B 127 TYR 0.013 0.001 TYR E 169 ARG 0.007 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 333 time to evaluate : 1.756 Fit side-chains REVERT: A 68 LYS cc_start: 0.8271 (mttm) cc_final: 0.8068 (mttm) REVERT: A 176 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7928 (mtp) REVERT: B 47 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.5675 (ppp) REVERT: D 299 MET cc_start: 0.8931 (mtm) cc_final: 0.8687 (mtm) REVERT: E 107 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7750 (tt0) outliers start: 54 outliers final: 13 residues processed: 361 average time/residue: 1.5500 time to fit residues: 603.0838 Evaluate side-chains 314 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 298 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.0050 chunk 139 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 49 GLN B 59 GLN B 162 ASN B 297 ASN C 78 ASN C 162 ASN D 12 ASN D 78 ASN D 115 ASN D 162 ASN D 297 ASN D 353 GLN E 78 ASN E 280 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14960 Z= 0.215 Angle : 0.547 6.009 20305 Z= 0.262 Chirality : 0.045 0.138 2255 Planarity : 0.004 0.036 2595 Dihedral : 6.751 104.172 2085 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.13 % Allowed : 21.85 % Favored : 75.02 % 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: -0.09 (0.20), residues: 1830 helix: -0.40 (0.18), residues: 780 sheet: 0.98 (0.29), residues: 340 loop : 0.07 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 356 HIS 0.004 0.001 HIS E 173 PHE 0.012 0.001 PHE B 127 TYR 0.006 0.001 TYR D 240 ARG 0.007 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 321 time to evaluate : 1.792 Fit side-chains REVERT: A 68 LYS cc_start: 0.8285 (mttm) cc_final: 0.8080 (mttm) REVERT: B 47 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.5641 (ppp) REVERT: B 225 ASN cc_start: 0.8086 (m-40) cc_final: 0.7862 (m-40) REVERT: D 176 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: D 299 MET cc_start: 0.8928 (mtm) cc_final: 0.8670 (mtm) outliers start: 49 outliers final: 19 residues processed: 344 average time/residue: 1.5878 time to fit residues: 587.2916 Evaluate side-chains 319 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 298 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 0.0570 chunk 48 optimal weight: 0.7980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 78 ASN B 162 ASN B 297 ASN C 246 GLN C 353 GLN D 12 ASN D 78 ASN D 115 ASN D 162 ASN D 297 ASN E 78 ASN E 371 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14960 Z= 0.189 Angle : 0.531 6.672 20305 Z= 0.252 Chirality : 0.044 0.134 2255 Planarity : 0.004 0.030 2595 Dihedral : 6.166 90.795 2085 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.49 % Allowed : 22.43 % Favored : 75.08 % 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: 0.22 (0.20), residues: 1830 helix: -0.10 (0.19), residues: 770 sheet: 0.98 (0.28), residues: 365 loop : 0.22 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 79 HIS 0.004 0.001 HIS E 173 PHE 0.011 0.001 PHE C 255 TYR 0.006 0.001 TYR C 188 ARG 0.005 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 303 time to evaluate : 1.678 Fit side-chains REVERT: A 68 LYS cc_start: 0.8286 (mttm) cc_final: 0.8082 (mttm) REVERT: A 176 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7877 (mtt) REVERT: B 47 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.5680 (ppp) REVERT: B 225 ASN cc_start: 0.8091 (m-40) cc_final: 0.7865 (m-40) REVERT: D 299 MET cc_start: 0.8927 (mtm) cc_final: 0.8578 (mtm) REVERT: E 78 ASN cc_start: 0.8446 (t0) cc_final: 0.8237 (t0) outliers start: 39 outliers final: 18 residues processed: 324 average time/residue: 1.6592 time to fit residues: 576.0700 Evaluate side-chains 330 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 310 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 152 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 162 ASN C 246 GLN C 263 GLN C 353 GLN D 12 ASN D 78 ASN D 115 ASN D 162 ASN D 297 ASN D 353 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14960 Z= 0.371 Angle : 0.595 7.080 20305 Z= 0.289 Chirality : 0.049 0.177 2255 Planarity : 0.005 0.058 2595 Dihedral : 6.609 95.808 2085 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.58 % Allowed : 21.09 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.20), residues: 1830 helix: -0.19 (0.18), residues: 780 sheet: 0.69 (0.28), residues: 335 loop : 0.14 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 340 HIS 0.006 0.002 HIS D 101 PHE 0.016 0.002 PHE C 127 TYR 0.008 0.001 TYR D 240 ARG 0.010 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 323 time to evaluate : 1.694 Fit side-chains REVERT: A 176 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7931 (mtt) REVERT: A 349 LEU cc_start: 0.8819 (mt) cc_final: 0.8548 (mp) REVERT: B 47 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5703 (ppp) REVERT: B 225 ASN cc_start: 0.8109 (m-40) cc_final: 0.7868 (m-40) REVERT: C 314 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: D 176 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8025 (mtp) REVERT: D 299 MET cc_start: 0.8960 (mtm) cc_final: 0.8645 (mtm) REVERT: E 107 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: E 113 LYS cc_start: 0.8365 (mmmm) cc_final: 0.7890 (mmtm) outliers start: 56 outliers final: 29 residues processed: 346 average time/residue: 1.6671 time to fit residues: 618.8216 Evaluate side-chains 355 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 321 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 269 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 59 GLN B 162 ASN C 246 GLN C 263 GLN C 353 GLN D 12 ASN D 78 ASN D 115 ASN D 162 ASN D 297 ASN E 78 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14960 Z= 0.190 Angle : 0.530 6.387 20305 Z= 0.253 Chirality : 0.044 0.136 2255 Planarity : 0.004 0.055 2595 Dihedral : 6.095 87.200 2085 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.75 % Allowed : 22.75 % Favored : 74.50 % 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: 0.29 (0.20), residues: 1830 helix: 0.06 (0.19), residues: 770 sheet: 0.84 (0.28), residues: 360 loop : 0.23 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.004 0.001 HIS D 161 PHE 0.011 0.001 PHE C 255 TYR 0.006 0.001 TYR C 240 ARG 0.007 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 321 time to evaluate : 1.960 Fit side-chains REVERT: B 47 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.5731 (ppp) REVERT: B 132 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8143 (ttp) REVERT: C 147 ARG cc_start: 0.8766 (ptp-170) cc_final: 0.8525 (ptp-110) REVERT: C 314 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: D 299 MET cc_start: 0.8957 (mtm) cc_final: 0.8634 (mtm) REVERT: D 326 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7964 (mptp) REVERT: E 113 LYS cc_start: 0.8369 (mmmm) cc_final: 0.7906 (mmtm) outliers start: 43 outliers final: 22 residues processed: 339 average time/residue: 1.6612 time to fit residues: 603.3436 Evaluate side-chains 340 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 314 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 297 ASN B 59 GLN B 162 ASN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 12 ASN D 78 ASN D 115 ASN D 162 ASN D 297 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 14960 Z= 0.466 Angle : 0.623 7.055 20305 Z= 0.303 Chirality : 0.051 0.176 2255 Planarity : 0.005 0.052 2595 Dihedral : 6.621 93.448 2085 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.19 % Allowed : 21.60 % Favored : 75.21 % 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: 0.01 (0.20), residues: 1830 helix: -0.15 (0.19), residues: 780 sheet: 0.63 (0.28), residues: 340 loop : 0.11 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.006 0.002 HIS D 101 PHE 0.018 0.002 PHE B 127 TYR 0.009 0.001 TYR C 240 ARG 0.013 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 309 time to evaluate : 1.610 Fit side-chains REVERT: A 176 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7968 (mtt) REVERT: A 314 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: B 47 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.5868 (ppp) REVERT: B 225 ASN cc_start: 0.8124 (m-40) cc_final: 0.7891 (m-40) REVERT: B 305 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8465 (mmt) REVERT: C 147 ARG cc_start: 0.8808 (ptp-170) cc_final: 0.8560 (ptp-110) REVERT: C 314 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: D 176 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: D 299 MET cc_start: 0.8981 (mtm) cc_final: 0.8676 (mtm) outliers start: 50 outliers final: 27 residues processed: 328 average time/residue: 1.6368 time to fit residues: 575.1599 Evaluate side-chains 341 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 308 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 162 ASN C 246 GLN C 263 GLN C 353 GLN D 12 ASN D 78 ASN D 115 ASN D 162 ASN D 297 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14960 Z= 0.186 Angle : 0.533 6.183 20305 Z= 0.254 Chirality : 0.044 0.136 2255 Planarity : 0.004 0.044 2595 Dihedral : 6.029 86.747 2085 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.30 % Allowed : 23.00 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.20), residues: 1830 helix: 0.11 (0.19), residues: 770 sheet: 0.79 (0.27), residues: 360 loop : 0.20 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.004 0.001 HIS D 161 PHE 0.011 0.001 PHE A 255 TYR 0.006 0.001 TYR A 69 ARG 0.011 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 313 time to evaluate : 1.780 Fit side-chains REVERT: A 28 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7910 (ttp-170) REVERT: B 47 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.5825 (ppp) REVERT: C 147 ARG cc_start: 0.8748 (ptp-170) cc_final: 0.8527 (ptp-110) REVERT: C 314 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: D 299 MET cc_start: 0.8964 (mtm) cc_final: 0.8651 (mtm) outliers start: 36 outliers final: 21 residues processed: 326 average time/residue: 1.7096 time to fit residues: 597.3885 Evaluate side-chains 323 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 299 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 137 GLN A 297 ASN B 59 GLN B 162 ASN C 246 GLN C 263 GLN C 353 GLN D 12 ASN D 78 ASN D 115 ASN D 162 ASN D 297 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14960 Z= 0.444 Angle : 0.622 6.759 20305 Z= 0.302 Chirality : 0.051 0.158 2255 Planarity : 0.005 0.057 2595 Dihedral : 6.564 94.631 2085 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.88 % Allowed : 22.43 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.00 (0.20), residues: 1830 helix: -0.13 (0.19), residues: 780 sheet: 0.60 (0.28), residues: 340 loop : 0.09 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.005 0.002 HIS D 101 PHE 0.018 0.002 PHE B 127 TYR 0.009 0.001 TYR C 240 ARG 0.014 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 308 time to evaluate : 1.631 Fit side-chains REVERT: A 28 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7907 (ttp-170) REVERT: A 176 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7965 (mtt) REVERT: A 314 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: B 47 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.5940 (ppp) REVERT: C 147 ARG cc_start: 0.8775 (ptp-170) cc_final: 0.8549 (ptp-110) REVERT: C 314 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: D 176 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8028 (mtp) REVERT: D 299 MET cc_start: 0.8986 (mtm) cc_final: 0.8682 (mtm) REVERT: E 113 LYS cc_start: 0.6268 (mptt) cc_final: 0.5816 (mptt) outliers start: 45 outliers final: 27 residues processed: 323 average time/residue: 1.7139 time to fit residues: 593.1399 Evaluate side-chains 342 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 309 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 336 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 59 GLN B 162 ASN C 246 GLN C 263 GLN C 353 GLN D 12 ASN D 78 ASN D 115 ASN D 162 ASN D 297 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 78 ASN E 137 GLN E 246 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14960 Z= 0.177 Angle : 0.537 6.236 20305 Z= 0.256 Chirality : 0.044 0.134 2255 Planarity : 0.004 0.056 2595 Dihedral : 5.946 85.651 2085 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.79 % Allowed : 23.26 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.20), residues: 1830 helix: 0.14 (0.19), residues: 770 sheet: 0.78 (0.27), residues: 360 loop : 0.21 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.004 0.001 HIS D 161 PHE 0.012 0.001 PHE A 255 TYR 0.006 0.001 TYR C 143 ARG 0.013 0.000 ARG B 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 306 time to evaluate : 1.677 Fit side-chains REVERT: B 47 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.5890 (ppp) REVERT: C 147 ARG cc_start: 0.8709 (ptp-170) cc_final: 0.8493 (ptp-110) REVERT: D 299 MET cc_start: 0.8964 (mtm) cc_final: 0.8655 (mtm) REVERT: E 113 LYS cc_start: 0.6581 (mptt) cc_final: 0.6259 (mptt) outliers start: 28 outliers final: 21 residues processed: 318 average time/residue: 1.6444 time to fit residues: 560.4202 Evaluate side-chains 329 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 307 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 59 GLN B 162 ASN C 246 GLN C 263 GLN C 353 GLN D 78 ASN D 115 ASN D 162 ASN D 297 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099450 restraints weight = 18855.032| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.16 r_work: 0.3376 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14960 Z= 0.396 Angle : 0.606 6.487 20305 Z= 0.294 Chirality : 0.049 0.161 2255 Planarity : 0.005 0.057 2595 Dihedral : 6.422 93.847 2085 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.36 % Allowed : 22.75 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.20), residues: 1830 helix: -0.05 (0.19), residues: 780 sheet: 0.57 (0.28), residues: 335 loop : 0.12 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 340 HIS 0.005 0.002 HIS A 101 PHE 0.017 0.002 PHE B 127 TYR 0.008 0.001 TYR C 240 ARG 0.013 0.001 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8162.67 seconds wall clock time: 143 minutes 12.55 seconds (8592.55 seconds total)