Starting phenix.real_space_refine on Sat Jul 20 20:29:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/07_2024/6kln_0712_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/07_2024/6kln_0712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/07_2024/6kln_0712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/07_2024/6kln_0712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/07_2024/6kln_0712_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kln_0712/07_2024/6kln_0712_neut.cif" } resolution = 3.4 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= -0.000 sd= 0.003 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 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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} Time building chain proxies: 7.05, per 1000 atoms: 0.60 Number of scatterers: 11748 At special positions: 0 Unit cell: (92.02, 96.3, 165.85, 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 84 16.00 P 8 15.00 Mg 4 11.99 O 2264 8.00 N 1980 7.00 C 7408 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: 4.40 Conformation dependent library (CDL) restraints added in 2.1 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 20 sheets defined 43.3% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.636A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.116A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.759A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.579A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.537A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.930A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.748A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.749A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.633A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.645A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.862A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.607A pdb=" N GLY A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.066A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.636A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.116A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.758A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.578A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.537A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.931A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.748A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.750A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.633A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.645A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.862A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.607A pdb=" N GLY B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 366 through 370 removed outlier: 4.067A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.636A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.117A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.759A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.578A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.537A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.931A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.748A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.750A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.633A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.645A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.863A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.608A pdb=" N GLY C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 366 through 370 removed outlier: 4.066A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.636A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.117A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.758A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.579A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.536A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.930A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.748A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 275 through 283 removed outlier: 3.750A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.633A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.645A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.863A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.607A pdb=" N GLY D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 366 through 370 removed outlier: 4.067A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.181A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.920A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.182A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.920A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 7.181A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.921A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 7.181A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.920A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 404 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 4.86 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: 3840 1.34 - 1.46: 2624 1.46 - 1.58: 5380 1.58 - 1.70: 12 1.70 - 1.82: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.398 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" CG HIC D 73 " pdb=" CD2 HIC D 73 " ideal model delta sigma weight residual 1.369 1.407 -0.038 2.00e-02 2.50e+03 3.61e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.13: 370 106.13 - 113.43: 6688 113.43 - 120.72: 5471 120.72 - 128.01: 3644 128.01 - 135.31: 119 Bond angle restraints: 16292 Sorted by residual: angle pdb=" N ILE A 267 " pdb=" CA ILE A 267 " pdb=" C ILE A 267 " ideal model delta sigma weight residual 111.91 108.86 3.05 8.90e-01 1.26e+00 1.18e+01 angle pdb=" N ILE C 267 " pdb=" CA ILE C 267 " pdb=" C ILE C 267 " ideal model delta sigma weight residual 111.91 108.89 3.02 8.90e-01 1.26e+00 1.15e+01 angle pdb=" N ILE B 267 " pdb=" CA ILE B 267 " pdb=" C ILE B 267 " ideal model delta sigma weight residual 111.91 108.91 3.00 8.90e-01 1.26e+00 1.14e+01 angle pdb=" N ILE D 267 " pdb=" CA ILE D 267 " pdb=" C ILE D 267 " ideal model delta sigma weight residual 111.91 108.92 2.99 8.90e-01 1.26e+00 1.13e+01 angle pdb=" C ALA C 22 " pdb=" N GLY C 23 " pdb=" CA GLY C 23 " ideal model delta sigma weight residual 123.30 120.24 3.06 1.06e+00 8.90e-01 8.34e+00 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6296 17.74 - 35.48: 736 35.48 - 53.21: 128 53.21 - 70.95: 48 70.95 - 88.69: 12 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" CA SER D 232 " pdb=" C SER D 232 " pdb=" N SER D 233 " pdb=" CA SER D 233 " ideal model delta harmonic sigma weight residual -180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA SER A 232 " pdb=" C SER A 232 " pdb=" N SER A 233 " pdb=" CA SER A 233 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA SER C 232 " pdb=" C SER C 232 " pdb=" N SER C 233 " pdb=" CA SER C 233 " ideal model delta harmonic sigma weight residual 180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 853 0.035 - 0.070: 612 0.070 - 0.105: 246 0.105 - 0.140: 93 0.140 - 0.175: 4 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB VAL D 152 " pdb=" CA VAL D 152 " pdb=" CG1 VAL D 152 " pdb=" CG2 VAL D 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB VAL B 152 " pdb=" CA VAL B 152 " pdb=" CG1 VAL B 152 " pdb=" CG2 VAL B 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CB VAL A 152 " pdb=" CA VAL A 152 " pdb=" CG1 VAL A 152 " pdb=" CG2 VAL A 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 270 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.36e+00 pdb=" C GLU B 270 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU B 270 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 271 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 270 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C GLU A 270 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU A 270 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 271 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 243 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.022 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 111 2.50 - 3.10: 8514 3.10 - 3.70: 17100 3.70 - 4.30: 25426 4.30 - 4.90: 43623 Nonbonded interactions: 94774 Sorted by model distance: nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 1.903 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 1.903 2.170 nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 1.904 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 1.904 2.170 nonbonded pdb=" O SER A 33 " pdb=" OG SER A 33 " model vdw 2.168 2.440 ... (remaining 94769 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' } 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: 0.730 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 34.330 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 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 : 0.009 0.058 12004 Z= 0.606 Angle : 0.859 8.181 16292 Z= 0.486 Chirality : 0.053 0.175 1808 Planarity : 0.004 0.038 2084 Dihedral : 16.338 88.687 4468 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 11.46 % Allowed : 9.71 % Favored : 78.82 % 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: -4.65 (0.17), residues: 1468 helix: -3.50 (0.15), residues: 580 sheet: -2.92 (0.28), residues: 220 loop : -2.59 (0.19), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 101 PHE 0.009 0.002 PHE D 375 TYR 0.009 0.001 TYR A 69 ARG 0.004 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 80 time to evaluate : 1.397 Fit side-chains REVERT: A 44 MET cc_start: 0.8157 (mmt) cc_final: 0.7043 (pmm) REVERT: A 152 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8761 (p) REVERT: B 66 THR cc_start: 0.9648 (OUTLIER) cc_final: 0.9425 (t) REVERT: B 132 MET cc_start: 0.9097 (ppp) cc_final: 0.8814 (ppp) REVERT: B 167 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: B 249 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9288 (p) REVERT: B 351 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9074 (p) REVERT: C 44 MET cc_start: 0.7316 (mmt) cc_final: 0.6958 (tpp) REVERT: C 82 MET cc_start: 0.9121 (tpt) cc_final: 0.8469 (tmm) REVERT: C 277 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8578 (m) REVERT: C 303 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.9175 (p) REVERT: C 326 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8476 (mtpp) REVERT: D 47 MET cc_start: 0.5019 (OUTLIER) cc_final: 0.4662 (mpp) REVERT: D 152 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9012 (m) outliers start: 144 outliers final: 34 residues processed: 217 average time/residue: 0.1979 time to fit residues: 64.7422 Evaluate side-chains 111 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 67 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 0.0030 chunk 134 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 161 HIS A 162 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 161 HIS ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 161 HIS C 162 ASN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 161 HIS D 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12004 Z= 0.143 Angle : 0.584 5.964 16292 Z= 0.287 Chirality : 0.044 0.126 1808 Planarity : 0.004 0.032 2084 Dihedral : 8.539 69.197 1725 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.71 % Allowed : 13.61 % Favored : 83.68 % 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: -2.97 (0.20), residues: 1468 helix: -2.01 (0.20), residues: 568 sheet: -2.05 (0.29), residues: 228 loop : -1.74 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 340 HIS 0.004 0.001 HIS A 87 PHE 0.021 0.001 PHE A 223 TYR 0.010 0.001 TYR D 306 ARG 0.004 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 69 time to evaluate : 1.455 Fit side-chains REVERT: A 44 MET cc_start: 0.8110 (mmt) cc_final: 0.6685 (pmm) REVERT: A 82 MET cc_start: 0.8418 (mmm) cc_final: 0.8056 (tmm) REVERT: A 303 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9094 (m) REVERT: B 44 MET cc_start: 0.7957 (mmm) cc_final: 0.6641 (ptp) REVERT: B 132 MET cc_start: 0.8898 (ppp) cc_final: 0.8676 (ppp) REVERT: B 249 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9268 (p) REVERT: C 82 MET cc_start: 0.9182 (tpt) cc_final: 0.8784 (tmm) REVERT: C 176 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7642 (mtt) REVERT: D 47 MET cc_start: 0.5171 (mtm) cc_final: 0.4617 (mpp) REVERT: D 227 MET cc_start: 0.9003 (tpp) cc_final: 0.8542 (tpp) outliers start: 34 outliers final: 14 residues processed: 97 average time/residue: 0.1855 time to fit residues: 29.1341 Evaluate side-chains 83 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 149 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 20.0000 chunk 41 optimal weight: 0.1980 chunk 111 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 354 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12004 Z= 0.213 Angle : 0.573 7.665 16292 Z= 0.273 Chirality : 0.044 0.129 1808 Planarity : 0.003 0.029 2084 Dihedral : 7.116 63.720 1686 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.99 % Allowed : 13.69 % Favored : 84.32 % 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: -1.97 (0.21), residues: 1468 helix: -1.15 (0.22), residues: 564 sheet: -1.42 (0.32), residues: 228 loop : -1.25 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS A 87 PHE 0.015 0.001 PHE A 223 TYR 0.010 0.001 TYR A 166 ARG 0.004 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 1.329 Fit side-chains REVERT: A 44 MET cc_start: 0.8005 (mmt) cc_final: 0.7186 (pmm) REVERT: A 227 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8985 (mpp) REVERT: B 44 MET cc_start: 0.7991 (mmm) cc_final: 0.6753 (ptp) REVERT: B 132 MET cc_start: 0.8876 (ppp) cc_final: 0.8612 (ppp) REVERT: C 44 MET cc_start: 0.7215 (tpp) cc_final: 0.6909 (tpp) REVERT: C 82 MET cc_start: 0.9303 (tpt) cc_final: 0.8787 (tmm) REVERT: C 132 MET cc_start: 0.8933 (ptm) cc_final: 0.8718 (ptm) REVERT: C 176 MET cc_start: 0.7941 (mtt) cc_final: 0.7707 (mtt) REVERT: C 227 MET cc_start: 0.9473 (tpp) cc_final: 0.9182 (tpp) REVERT: C 283 MET cc_start: 0.8719 (mmm) cc_final: 0.8281 (mmm) REVERT: D 47 MET cc_start: 0.5107 (mtm) cc_final: 0.4538 (mpp) REVERT: D 227 MET cc_start: 0.9184 (tpp) cc_final: 0.8747 (tpp) outliers start: 25 outliers final: 14 residues processed: 91 average time/residue: 0.2021 time to fit residues: 29.2916 Evaluate side-chains 82 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 0.0470 chunk 135 optimal weight: 0.0170 chunk 143 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN C 59 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12004 Z= 0.151 Angle : 0.533 8.358 16292 Z= 0.249 Chirality : 0.043 0.126 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.696 82.306 1680 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.19 % Allowed : 14.49 % Favored : 84.32 % 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: -1.34 (0.22), residues: 1468 helix: -0.62 (0.23), residues: 564 sheet: -1.06 (0.34), residues: 228 loop : -0.91 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.004 0.001 HIS A 87 PHE 0.010 0.001 PHE A 375 TYR 0.008 0.001 TYR B 279 ARG 0.002 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.341 Fit side-chains REVERT: A 44 MET cc_start: 0.8320 (mmt) cc_final: 0.7239 (pmm) REVERT: B 44 MET cc_start: 0.7948 (mmm) cc_final: 0.6770 (ptp) REVERT: C 82 MET cc_start: 0.9310 (tpt) cc_final: 0.8760 (tmm) REVERT: C 132 MET cc_start: 0.8868 (ptm) cc_final: 0.8637 (ptm) REVERT: C 227 MET cc_start: 0.9429 (tpp) cc_final: 0.9188 (tpp) REVERT: C 325 MET cc_start: 0.8486 (ppp) cc_final: 0.8174 (ppp) REVERT: D 47 MET cc_start: 0.5059 (mtm) cc_final: 0.4472 (mpp) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.2016 time to fit residues: 26.2914 Evaluate side-chains 78 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 2 optimal weight: 0.0170 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 0.4980 chunk 128 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 overall best weight: 4.7024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12004 Z= 0.288 Angle : 0.584 8.193 16292 Z= 0.278 Chirality : 0.045 0.137 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.645 82.229 1678 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.04 % Allowed : 14.81 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.22), residues: 1468 helix: -0.23 (0.23), residues: 564 sheet: -0.80 (0.35), residues: 236 loop : -0.57 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.004 0.001 HIS A 87 PHE 0.009 0.001 PHE B 223 TYR 0.011 0.001 TYR A 166 ARG 0.002 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.370 Fit side-chains REVERT: A 44 MET cc_start: 0.8357 (mmt) cc_final: 0.7246 (pmm) REVERT: B 44 MET cc_start: 0.7966 (mmm) cc_final: 0.6802 (ptp) REVERT: C 82 MET cc_start: 0.9379 (tpt) cc_final: 0.8725 (tmm) REVERT: C 132 MET cc_start: 0.9060 (ptm) cc_final: 0.8770 (ptm) REVERT: D 47 MET cc_start: 0.5041 (mtm) cc_final: 0.4498 (mpp) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.2275 time to fit residues: 28.5493 Evaluate side-chains 77 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 143 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12004 Z= 0.234 Angle : 0.553 7.661 16292 Z= 0.261 Chirality : 0.044 0.129 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.454 80.895 1676 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.88 % Allowed : 15.68 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.23), residues: 1468 helix: 0.08 (0.23), residues: 564 sheet: -0.77 (0.34), residues: 244 loop : -0.31 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.003 0.001 HIS A 87 PHE 0.011 0.001 PHE C 223 TYR 0.009 0.001 TYR A 166 ARG 0.002 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 1.456 Fit side-chains REVERT: A 44 MET cc_start: 0.8257 (mmt) cc_final: 0.6993 (pmm) REVERT: A 47 MET cc_start: 0.4479 (mmt) cc_final: 0.4149 (mmm) REVERT: A 132 MET cc_start: 0.8461 (tmm) cc_final: 0.8036 (tmm) REVERT: B 44 MET cc_start: 0.7950 (mmm) cc_final: 0.6794 (ptp) REVERT: B 132 MET cc_start: 0.8867 (ppp) cc_final: 0.8484 (ppp) REVERT: C 82 MET cc_start: 0.9366 (tpt) cc_final: 0.8746 (tmm) REVERT: C 132 MET cc_start: 0.9006 (ptm) cc_final: 0.8725 (ptm) REVERT: D 44 MET cc_start: 0.8118 (mmm) cc_final: 0.7831 (mmm) outliers start: 11 outliers final: 10 residues processed: 78 average time/residue: 0.2118 time to fit residues: 25.8032 Evaluate side-chains 77 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 88 optimal weight: 9.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12004 Z= 0.281 Angle : 0.585 7.475 16292 Z= 0.279 Chirality : 0.045 0.150 1808 Planarity : 0.003 0.029 2084 Dihedral : 6.444 78.797 1675 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.19 % Allowed : 16.08 % Favored : 82.72 % 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: -0.30 (0.23), residues: 1468 helix: 0.18 (0.23), residues: 564 sheet: -0.73 (0.35), residues: 244 loop : -0.14 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.003 0.001 HIS A 87 PHE 0.015 0.001 PHE C 223 TYR 0.022 0.001 TYR B 279 ARG 0.002 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.346 Fit side-chains REVERT: A 44 MET cc_start: 0.8294 (mmt) cc_final: 0.7019 (pmm) REVERT: A 47 MET cc_start: 0.4522 (mmt) cc_final: 0.4253 (mmm) REVERT: A 132 MET cc_start: 0.8478 (tmm) cc_final: 0.8023 (tmm) REVERT: B 44 MET cc_start: 0.8038 (mmm) cc_final: 0.6863 (ptp) REVERT: B 283 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8530 (mpp) REVERT: C 82 MET cc_start: 0.9372 (tpt) cc_final: 0.8748 (tmm) REVERT: C 132 MET cc_start: 0.8937 (ptm) cc_final: 0.8639 (ptm) REVERT: D 227 MET cc_start: 0.9435 (tpp) cc_final: 0.8833 (mpp) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 0.2040 time to fit residues: 26.2351 Evaluate side-chains 79 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 HIS ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12004 Z= 0.337 Angle : 0.611 7.470 16292 Z= 0.293 Chirality : 0.045 0.161 1808 Planarity : 0.004 0.028 2084 Dihedral : 6.478 77.474 1674 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.19 % Allowed : 16.64 % Favored : 82.17 % 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: -0.23 (0.23), residues: 1468 helix: 0.26 (0.24), residues: 564 sheet: -0.73 (0.35), residues: 244 loop : -0.08 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 79 HIS 0.003 0.001 HIS A 87 PHE 0.014 0.001 PHE C 223 TYR 0.027 0.001 TYR B 279 ARG 0.003 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.390 Fit side-chains REVERT: A 44 MET cc_start: 0.8357 (mmt) cc_final: 0.7101 (pmm) REVERT: A 82 MET cc_start: 0.8857 (tpt) cc_final: 0.8618 (tpt) REVERT: A 132 MET cc_start: 0.8471 (tmm) cc_final: 0.8042 (tmm) REVERT: B 44 MET cc_start: 0.8022 (mmm) cc_final: 0.6880 (ptp) REVERT: B 132 MET cc_start: 0.8918 (ppp) cc_final: 0.8510 (ppp) REVERT: B 283 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8479 (mpp) REVERT: C 82 MET cc_start: 0.9379 (tpt) cc_final: 0.8795 (tmm) REVERT: C 132 MET cc_start: 0.8995 (ptm) cc_final: 0.8737 (ptm) REVERT: C 283 MET cc_start: 0.8771 (mmm) cc_final: 0.8434 (mmm) REVERT: D 227 MET cc_start: 0.9421 (tpp) cc_final: 0.8845 (mpp) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.1921 time to fit residues: 24.7836 Evaluate side-chains 80 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12004 Z= 0.286 Angle : 0.585 7.574 16292 Z= 0.279 Chirality : 0.045 0.157 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.394 76.650 1674 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.19 % Allowed : 17.12 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.23), residues: 1468 helix: 0.35 (0.24), residues: 564 sheet: -0.71 (0.35), residues: 244 loop : -0.09 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS A 87 PHE 0.015 0.001 PHE C 223 TYR 0.025 0.001 TYR B 279 ARG 0.003 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.360 Fit side-chains REVERT: A 44 MET cc_start: 0.8183 (mmt) cc_final: 0.7212 (pmm) REVERT: A 132 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8030 (tmm) REVERT: B 44 MET cc_start: 0.7979 (mmm) cc_final: 0.6842 (ptp) REVERT: B 132 MET cc_start: 0.8899 (ppp) cc_final: 0.8490 (ppp) REVERT: B 283 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8498 (mpp) REVERT: C 132 MET cc_start: 0.8975 (ptm) cc_final: 0.8694 (ptm) REVERT: C 283 MET cc_start: 0.8822 (mmm) cc_final: 0.8477 (mmm) REVERT: D 227 MET cc_start: 0.9415 (tpp) cc_final: 0.8876 (mpp) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.2047 time to fit residues: 25.8464 Evaluate side-chains 81 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12004 Z= 0.267 Angle : 0.576 7.456 16292 Z= 0.274 Chirality : 0.045 0.155 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.292 75.529 1674 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.19 % Allowed : 16.96 % Favored : 81.85 % 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 (0.23), residues: 1468 helix: 0.46 (0.24), residues: 568 sheet: -0.67 (0.35), residues: 244 loop : -0.04 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.004 0.001 HIS C 87 PHE 0.017 0.001 PHE C 223 TYR 0.025 0.001 TYR B 279 ARG 0.003 0.000 ARG A 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.346 Fit side-chains REVERT: A 44 MET cc_start: 0.8203 (mmt) cc_final: 0.7248 (pmm) REVERT: A 132 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8036 (tmm) REVERT: B 44 MET cc_start: 0.8027 (mmm) cc_final: 0.6946 (ptp) REVERT: B 132 MET cc_start: 0.8900 (ppp) cc_final: 0.8486 (ppp) REVERT: B 283 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8506 (mpp) REVERT: C 82 MET cc_start: 0.9158 (mmm) cc_final: 0.8554 (tmm) REVERT: C 132 MET cc_start: 0.8971 (ptm) cc_final: 0.8689 (ptm) REVERT: C 283 MET cc_start: 0.8788 (mmm) cc_final: 0.8433 (mmm) REVERT: D 227 MET cc_start: 0.9407 (tpp) cc_final: 0.8911 (mpp) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.2032 time to fit residues: 25.9862 Evaluate side-chains 83 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.033422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.027393 restraints weight = 76654.374| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 3.97 r_work: 0.2475 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12004 Z= 0.289 Angle : 0.588 7.475 16292 Z= 0.280 Chirality : 0.045 0.157 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.317 74.673 1674 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.27 % Allowed : 17.12 % Favored : 81.61 % 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: -0.02 (0.23), residues: 1468 helix: 0.50 (0.24), residues: 568 sheet: -0.70 (0.35), residues: 244 loop : -0.02 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 79 HIS 0.003 0.001 HIS A 87 PHE 0.017 0.001 PHE C 223 TYR 0.025 0.001 TYR B 279 ARG 0.003 0.000 ARG A 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.21 seconds wall clock time: 35 minutes 40.83 seconds (2140.83 seconds total)