Starting phenix.real_space_refine on Sat Apr 6 23:49:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/04_2024/8xzj_38798_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/04_2024/8xzj_38798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/04_2024/8xzj_38798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/04_2024/8xzj_38798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/04_2024/8xzj_38798_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzj_38798/04_2024/8xzj_38798_updated.pdb" } resolution = 3.0 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= 0.002 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 5804 2.51 5 N 1536 2.21 5 O 1693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 313": "OD1" <-> "OD2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9106 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2410 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "L" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 112 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.16, per 1000 atoms: 0.57 Number of scatterers: 9106 At special positions: 0 Unit cell: (100.44, 132.06, 114.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1693 8.00 N 1536 7.00 C 5804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.16 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.11 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 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: 3.45 Conformation dependent library (CDL) restraints added in 1.8 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 14 sheets defined 35.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'R' and resid 25 through 54 removed outlier: 3.754A pdb=" N GLY R 28 " --> pdb=" O LYS R 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA R 29 " --> pdb=" O SER R 26 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE R 31 " --> pdb=" O GLY R 28 " (cutoff:3.500A) Proline residue: R 32 - end of helix removed outlier: 3.600A pdb=" N VAL R 38 " --> pdb=" O TYR R 35 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU R 41 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY R 42 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR R 43 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN R 46 " --> pdb=" O THR R 43 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP R 51 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL R 53 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 77 Processing helix chain 'R' and resid 80 through 90 Proline residue: R 83 - end of helix removed outlier: 3.608A pdb=" N THR R 89 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 131 Processing helix chain 'R' and resid 138 through 144 removed outlier: 3.855A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG R 143 " --> pdb=" O ARG R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 160 Processing helix chain 'R' and resid 162 through 167 Processing helix chain 'R' and resid 194 through 209 Processing helix chain 'R' and resid 211 through 215 removed outlier: 3.705A pdb=" N THR R 215 " --> pdb=" O VAL R 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 211 through 215' Processing helix chain 'R' and resid 227 through 231 Processing helix chain 'R' and resid 237 through 275 Proline residue: R 263 - end of helix removed outlier: 4.199A pdb=" N THR R 269 " --> pdb=" O HIS R 265 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU R 270 " --> pdb=" O LEU R 266 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER R 275 " --> pdb=" O TYR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 310 removed outlier: 3.801A pdb=" N PHE R 291 " --> pdb=" O MET R 288 " (cutoff:3.500A) Proline residue: R 292 - end of helix removed outlier: 3.599A pdb=" N THR R 295 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR R 299 " --> pdb=" O CYS R 296 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN R 301 " --> pdb=" O SER R 298 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN R 305 " --> pdb=" O SER R 302 " (cutoff:3.500A) Proline residue: R 306 - end of helix removed outlier: 4.222A pdb=" N TYR R 309 " --> pdb=" O PRO R 306 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA R 310 " --> pdb=" O PHE R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 324 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.520A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.231A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.873A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.801A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'R' and resid 168 through 172 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.719A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.830A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.839A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.771A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.669A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.728A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.449A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.623A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.115A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.459A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= N, first strand: chain 'S' and resid 214 through 219 removed outlier: 6.082A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 389 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: 2.68 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2196 1.33 - 1.45: 1991 1.45 - 1.57: 5015 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 9307 Sorted by residual: bond pdb=" N ARG L 2 " pdb=" CA ARG L 2 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.24e+01 bond pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 1.474 1.428 0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" N VAL R 79 " pdb=" CA VAL R 79 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.09e-02 8.42e+03 1.05e+01 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" C4A NAL L 11 " pdb=" C8A NAL L 11 " ideal model delta sigma weight residual 1.419 1.480 -0.061 2.00e-02 2.50e+03 9.34e+00 ... (remaining 9302 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.13: 265 107.13 - 113.93: 5184 113.93 - 120.74: 4070 120.74 - 127.54: 3002 127.54 - 134.34: 92 Bond angle restraints: 12613 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.23 103.54 9.69 1.24e+00 6.50e-01 6.11e+01 angle pdb=" C ASP R 313 " pdb=" N PRO R 314 " pdb=" CA PRO R 314 " ideal model delta sigma weight residual 119.32 126.59 -7.27 1.14e+00 7.69e-01 4.07e+01 angle pdb=" N LEU R 266 " pdb=" CA LEU R 266 " pdb=" C LEU R 266 " ideal model delta sigma weight residual 113.97 107.43 6.54 1.28e+00 6.10e-01 2.61e+01 angle pdb=" N GLN R 226 " pdb=" CA GLN R 226 " pdb=" C GLN R 226 " ideal model delta sigma weight residual 113.97 107.48 6.49 1.28e+00 6.10e-01 2.57e+01 angle pdb=" N LEU R 308 " pdb=" CA LEU R 308 " pdb=" C LEU R 308 " ideal model delta sigma weight residual 111.36 116.79 -5.43 1.09e+00 8.42e-01 2.48e+01 ... (remaining 12608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 5235 17.12 - 34.24: 178 34.24 - 51.35: 61 51.35 - 68.47: 19 68.47 - 85.59: 6 Dihedral angle restraints: 5499 sinusoidal: 2130 harmonic: 3369 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 176.96 -83.96 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CD ARG R 91 " pdb=" NE ARG R 91 " pdb=" CZ ARG R 91 " pdb=" NH1 ARG R 91 " ideal model delta sinusoidal sigma weight residual 0.00 -41.70 41.70 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 916 0.047 - 0.094: 303 0.094 - 0.141: 135 0.141 - 0.188: 58 0.188 - 0.235: 12 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL R 300 " pdb=" N VAL R 300 " pdb=" C VAL R 300 " pdb=" CB VAL R 300 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1421 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 91 " 0.723 9.50e-02 1.11e+02 3.24e-01 6.39e+01 pdb=" NE ARG R 91 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG R 91 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG R 91 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 91 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 8 " 0.022 2.00e-02 2.50e+03 4.50e-02 2.03e+01 pdb=" C LYS L 8 " -0.078 2.00e-02 2.50e+03 pdb=" O LYS L 8 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY L 9 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 75 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.59e+00 pdb=" C GLN B 75 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN B 75 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.018 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1988 2.78 - 3.31: 8730 3.31 - 3.84: 15433 3.84 - 4.37: 19380 4.37 - 4.90: 32326 Nonbonded interactions: 77857 Sorted by model distance: nonbonded pdb=" CD1 ILE R 68 " pdb=" O TYR R 309 " model vdw 2.252 3.460 nonbonded pdb=" O PRO R 280 " pdb=" N ASP R 282 " model vdw 2.272 2.520 nonbonded pdb=" OD1 ASP R 23 " pdb=" NZ LYS L 8 " model vdw 2.287 2.520 nonbonded pdb=" OD2 ASP R 75 " pdb=" ND2 ASN R 305 " model vdw 2.330 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.348 2.440 ... (remaining 77852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.620 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: 2.860 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.810 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 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 : 0.011 0.061 9307 Z= 0.682 Angle : 0.945 9.693 12613 Z= 0.660 Chirality : 0.064 0.235 1424 Planarity : 0.010 0.324 1588 Dihedral : 11.329 85.590 3312 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.84 % Favored : 97.89 % Rotamer: Outliers : 2.72 % Allowed : 2.32 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.36 (0.24), residues: 1139 helix: 0.19 (0.24), residues: 400 sheet: 0.82 (0.29), residues: 288 loop : 0.09 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 95 HIS 0.009 0.001 HIS B 91 PHE 0.024 0.001 PHE B 199 TYR 0.034 0.002 TYR B 105 ARG 0.013 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: R 78 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7687 (t80) REVERT: R 293 TYR cc_start: 0.6553 (m-80) cc_final: 0.6161 (m-80) REVERT: A 32 ARG cc_start: 0.7145 (mtm-85) cc_final: 0.6692 (mtm180) REVERT: A 186 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6221 (mt-10) REVERT: B 156 GLN cc_start: 0.8012 (mt0) cc_final: 0.7779 (mt0) REVERT: B 176 GLN cc_start: 0.8320 (mt0) cc_final: 0.8024 (mt0) REVERT: B 219 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6774 (mtm110) REVERT: B 294 CYS cc_start: 0.7664 (m) cc_final: 0.7318 (m) REVERT: B 325 MET cc_start: 0.8126 (mmt) cc_final: 0.7790 (mmm) REVERT: G 59 ASN cc_start: 0.7839 (t0) cc_final: 0.7583 (t0) REVERT: S 23 SER cc_start: 0.8030 (t) cc_final: 0.7778 (m) REVERT: S 85 SER cc_start: 0.8182 (m) cc_final: 0.7971 (p) REVERT: S 87 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6829 (mtt-85) REVERT: L 8 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6644 (pttm) outliers start: 27 outliers final: 8 residues processed: 240 average time/residue: 1.3160 time to fit residues: 335.1434 Evaluate side-chains 143 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN B 91 HIS B 293 ASN S 39 GLN S 130 GLN S 159 ASN S 167 GLN S 182 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9307 Z= 0.195 Angle : 0.564 7.816 12613 Z= 0.299 Chirality : 0.042 0.177 1424 Planarity : 0.004 0.037 1588 Dihedral : 6.091 55.435 1281 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.67 % Favored : 98.16 % Rotamer: Outliers : 3.53 % Allowed : 10.79 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.00 (0.25), residues: 1139 helix: 1.14 (0.26), residues: 411 sheet: 0.86 (0.30), residues: 274 loop : 0.25 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.025 0.002 PHE R 110 TYR 0.019 0.002 TYR R 299 ARG 0.007 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.047 Fit side-chains REVERT: R 36 MET cc_start: 0.4935 (tpt) cc_final: 0.2817 (tmm) REVERT: R 93 TYR cc_start: 0.3547 (m-80) cc_final: 0.3329 (m-80) REVERT: R 162 MET cc_start: 0.6860 (ptt) cc_final: 0.6621 (ptt) REVERT: R 272 MET cc_start: 0.6181 (mtm) cc_final: 0.5693 (ptt) REVERT: R 293 TYR cc_start: 0.6471 (m-80) cc_final: 0.6181 (m-80) REVERT: A 198 MET cc_start: 0.7711 (ttm) cc_final: 0.7504 (ttp) REVERT: A 253 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7963 (mm) REVERT: A 274 PHE cc_start: 0.7087 (t80) cc_final: 0.6606 (t80) REVERT: B 19 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6488 (tpp-160) REVERT: B 138 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7220 (tt0) REVERT: B 212 ASP cc_start: 0.7711 (t0) cc_final: 0.7407 (t0) REVERT: B 217 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7962 (pmt) REVERT: B 219 ARG cc_start: 0.7012 (mtt-85) cc_final: 0.6730 (mtm110) REVERT: B 254 ASP cc_start: 0.6791 (t70) cc_final: 0.6544 (t0) REVERT: B 325 MET cc_start: 0.8088 (mmt) cc_final: 0.7518 (mmm) REVERT: G 20 LYS cc_start: 0.7668 (mtpt) cc_final: 0.7261 (mtpt) REVERT: S 23 SER cc_start: 0.8127 (t) cc_final: 0.7911 (m) REVERT: S 85 SER cc_start: 0.8191 (m) cc_final: 0.7946 (p) REVERT: S 87 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6817 (mtt-85) outliers start: 35 outliers final: 15 residues processed: 169 average time/residue: 1.2536 time to fit residues: 226.2883 Evaluate side-chains 147 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 ASN R 180 GLN A 311 ASN B 293 ASN S 159 ASN S 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9307 Z= 0.226 Angle : 0.546 8.239 12613 Z= 0.287 Chirality : 0.042 0.173 1424 Planarity : 0.004 0.038 1588 Dihedral : 5.188 51.541 1268 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.81 % Rotamer: Outliers : 3.33 % Allowed : 12.60 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.01 (0.25), residues: 1139 helix: 1.50 (0.27), residues: 395 sheet: 0.63 (0.30), residues: 283 loop : 0.10 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.027 0.002 PHE R 110 TYR 0.010 0.002 TYR S 178 ARG 0.008 0.000 ARG R 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: R 162 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6415 (ptt) REVERT: R 272 MET cc_start: 0.6209 (mtm) cc_final: 0.5788 (ptt) REVERT: R 293 TYR cc_start: 0.6387 (m-80) cc_final: 0.6111 (m-80) REVERT: A 46 LYS cc_start: 0.6717 (mtmm) cc_final: 0.6458 (mtpm) REVERT: A 184 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7628 (tt) REVERT: A 198 MET cc_start: 0.7780 (ttm) cc_final: 0.7565 (ttp) REVERT: A 208 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7619 (ttp-170) REVERT: A 274 PHE cc_start: 0.7065 (t80) cc_final: 0.6689 (t80) REVERT: B 19 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.6490 (tpp-160) REVERT: B 57 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8456 (mttt) REVERT: B 217 MET cc_start: 0.8377 (pmm) cc_final: 0.8016 (pmt) REVERT: B 219 ARG cc_start: 0.7032 (mtt-85) cc_final: 0.6743 (mtm110) REVERT: B 254 ASP cc_start: 0.6674 (t70) cc_final: 0.6439 (t0) REVERT: B 322 ASP cc_start: 0.7832 (m-30) cc_final: 0.7628 (m-30) REVERT: G 20 LYS cc_start: 0.7518 (mtpt) cc_final: 0.7125 (mtpt) REVERT: S 6 GLU cc_start: 0.7802 (mp0) cc_final: 0.7555 (mt-10) REVERT: S 23 SER cc_start: 0.8184 (t) cc_final: 0.7922 (m) REVERT: S 85 SER cc_start: 0.8178 (m) cc_final: 0.7799 (p) REVERT: S 87 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6788 (mtt90) REVERT: S 109 ASP cc_start: 0.7979 (p0) cc_final: 0.7773 (p0) REVERT: S 222 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7585 (pt0) outliers start: 33 outliers final: 14 residues processed: 158 average time/residue: 1.2837 time to fit residues: 216.0440 Evaluate side-chains 150 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 124 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 75 GLN B 176 GLN B 293 ASN S 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9307 Z= 0.226 Angle : 0.537 9.152 12613 Z= 0.281 Chirality : 0.042 0.149 1424 Planarity : 0.004 0.040 1588 Dihedral : 4.913 54.957 1266 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.02 % Favored : 97.89 % Rotamer: Outliers : 3.43 % Allowed : 13.31 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.97 (0.25), residues: 1139 helix: 1.47 (0.27), residues: 401 sheet: 0.55 (0.29), residues: 294 loop : 0.08 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.025 0.002 PHE R 110 TYR 0.010 0.002 TYR S 178 ARG 0.008 0.000 ARG R 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.085 Fit side-chains REVERT: R 101 PHE cc_start: 0.4348 (OUTLIER) cc_final: 0.4096 (m-10) REVERT: R 162 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6378 (ptt) REVERT: R 182 TYR cc_start: 0.6538 (p90) cc_final: 0.6250 (p90) REVERT: R 272 MET cc_start: 0.6212 (mtm) cc_final: 0.5735 (ptt) REVERT: R 293 TYR cc_start: 0.6378 (m-80) cc_final: 0.6175 (m-80) REVERT: A 21 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7448 (ttm110) REVERT: A 46 LYS cc_start: 0.6760 (mtmm) cc_final: 0.6521 (mtpm) REVERT: A 184 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 198 MET cc_start: 0.7787 (ttm) cc_final: 0.7586 (ttp) REVERT: A 208 ARG cc_start: 0.7891 (mtm110) cc_final: 0.7645 (ttp80) REVERT: A 274 PHE cc_start: 0.7138 (t80) cc_final: 0.6738 (t80) REVERT: A 310 LEU cc_start: 0.7743 (mp) cc_final: 0.7510 (mp) REVERT: B 19 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6342 (tpp-160) REVERT: B 57 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8430 (mttt) REVERT: B 177 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8057 (m) REVERT: B 217 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7984 (pmt) REVERT: B 219 ARG cc_start: 0.7040 (mtt-85) cc_final: 0.6754 (mtm110) REVERT: B 254 ASP cc_start: 0.6642 (t70) cc_final: 0.6392 (t0) REVERT: B 322 ASP cc_start: 0.7854 (m-30) cc_final: 0.7644 (m-30) REVERT: G 20 LYS cc_start: 0.7544 (mtpt) cc_final: 0.7155 (mtpt) REVERT: S 23 SER cc_start: 0.8174 (t) cc_final: 0.7947 (m) REVERT: S 85 SER cc_start: 0.8169 (m) cc_final: 0.7777 (p) REVERT: S 87 ARG cc_start: 0.7103 (mtt180) cc_final: 0.6761 (mtt90) REVERT: S 109 ASP cc_start: 0.7950 (p0) cc_final: 0.7732 (p0) outliers start: 34 outliers final: 15 residues processed: 158 average time/residue: 1.2794 time to fit residues: 215.8348 Evaluate side-chains 153 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 124 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN B 293 ASN S 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9307 Z= 0.204 Angle : 0.516 8.837 12613 Z= 0.271 Chirality : 0.041 0.146 1424 Planarity : 0.004 0.041 1588 Dihedral : 4.756 57.659 1264 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.02 % Favored : 97.89 % Rotamer: Outliers : 2.92 % Allowed : 16.13 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.03 (0.26), residues: 1139 helix: 1.51 (0.27), residues: 405 sheet: 0.54 (0.29), residues: 294 loop : 0.14 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.023 0.001 PHE R 110 TYR 0.010 0.001 TYR R 93 ARG 0.007 0.000 ARG R 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.034 Fit side-chains REVERT: R 54 PHE cc_start: 0.6515 (OUTLIER) cc_final: 0.6132 (m-10) REVERT: R 101 PHE cc_start: 0.4279 (OUTLIER) cc_final: 0.3995 (m-10) REVERT: R 139 ARG cc_start: 0.7326 (mtm-85) cc_final: 0.6806 (pmt-80) REVERT: R 162 MET cc_start: 0.6499 (ptt) cc_final: 0.6232 (ptt) REVERT: A 184 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7653 (tt) REVERT: A 198 MET cc_start: 0.7783 (ttm) cc_final: 0.7579 (ttp) REVERT: A 274 PHE cc_start: 0.7158 (t80) cc_final: 0.6815 (t80) REVERT: A 310 LEU cc_start: 0.7778 (mp) cc_final: 0.7542 (mp) REVERT: B 19 ARG cc_start: 0.7215 (ttp-110) cc_final: 0.6320 (tpp-160) REVERT: B 57 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8405 (mttt) REVERT: B 214 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5902 (mmt180) REVERT: B 217 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7927 (pmt) REVERT: B 219 ARG cc_start: 0.7065 (mtt-85) cc_final: 0.6764 (mtm110) REVERT: B 254 ASP cc_start: 0.6628 (t70) cc_final: 0.6369 (t0) REVERT: B 322 ASP cc_start: 0.7863 (m-30) cc_final: 0.7649 (m-30) REVERT: G 20 LYS cc_start: 0.7549 (mtpt) cc_final: 0.7175 (mtpt) REVERT: S 6 GLU cc_start: 0.7792 (mp0) cc_final: 0.7523 (mt-10) REVERT: S 23 SER cc_start: 0.8150 (t) cc_final: 0.7927 (m) REVERT: S 85 SER cc_start: 0.8165 (m) cc_final: 0.7784 (p) REVERT: S 87 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6757 (mtt90) REVERT: S 109 ASP cc_start: 0.7891 (p0) cc_final: 0.7671 (p0) REVERT: S 222 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7626 (pt0) outliers start: 29 outliers final: 16 residues processed: 154 average time/residue: 1.2972 time to fit residues: 213.0118 Evaluate side-chains 148 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 124 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN B 293 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9307 Z= 0.188 Angle : 0.514 9.696 12613 Z= 0.267 Chirality : 0.041 0.143 1424 Planarity : 0.004 0.040 1588 Dihedral : 4.675 59.829 1262 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.02 % Favored : 97.89 % Rotamer: Outliers : 2.62 % Allowed : 16.23 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.04 (0.26), residues: 1139 helix: 1.57 (0.27), residues: 405 sheet: 0.59 (0.29), residues: 289 loop : 0.05 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.023 0.001 PHE R 110 TYR 0.013 0.001 TYR R 35 ARG 0.007 0.000 ARG R 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.060 Fit side-chains REVERT: R 36 MET cc_start: 0.5967 (tpp) cc_final: 0.3388 (tmm) REVERT: R 54 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.6072 (m-10) REVERT: R 101 PHE cc_start: 0.4217 (OUTLIER) cc_final: 0.3994 (m-10) REVERT: R 139 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.6737 (pmt-80) REVERT: R 162 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.6183 (ptt) REVERT: R 293 TYR cc_start: 0.6495 (m-80) cc_final: 0.6253 (m-80) REVERT: A 184 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7670 (tt) REVERT: A 198 MET cc_start: 0.7786 (ttm) cc_final: 0.7586 (ttp) REVERT: A 274 PHE cc_start: 0.7172 (t80) cc_final: 0.6862 (t80) REVERT: A 310 LEU cc_start: 0.7792 (mp) cc_final: 0.7551 (mp) REVERT: B 19 ARG cc_start: 0.7275 (ttp-110) cc_final: 0.6401 (tpp-160) REVERT: B 57 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8375 (mttt) REVERT: B 217 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7901 (pmt) REVERT: B 219 ARG cc_start: 0.7074 (mtt-85) cc_final: 0.6776 (mtm110) REVERT: B 322 ASP cc_start: 0.7859 (m-30) cc_final: 0.7634 (m-30) REVERT: G 20 LYS cc_start: 0.7540 (mtpt) cc_final: 0.7173 (mtpt) REVERT: S 6 GLU cc_start: 0.7759 (mp0) cc_final: 0.7266 (mp0) REVERT: S 85 SER cc_start: 0.8152 (m) cc_final: 0.7795 (p) REVERT: S 87 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6752 (mtt90) REVERT: S 109 ASP cc_start: 0.7859 (p0) cc_final: 0.7632 (p0) REVERT: S 142 SER cc_start: 0.6858 (p) cc_final: 0.6381 (t) REVERT: S 222 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7646 (pt0) outliers start: 26 outliers final: 12 residues processed: 143 average time/residue: 1.3051 time to fit residues: 198.6821 Evaluate side-chains 142 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 124 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9307 Z= 0.184 Angle : 0.503 10.503 12613 Z= 0.262 Chirality : 0.041 0.140 1424 Planarity : 0.003 0.040 1588 Dihedral : 4.621 57.759 1262 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.02 % Favored : 97.89 % Rotamer: Outliers : 3.33 % Allowed : 16.13 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.06 (0.26), residues: 1139 helix: 1.63 (0.27), residues: 405 sheet: 0.57 (0.29), residues: 289 loop : 0.05 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.022 0.001 PHE R 110 TYR 0.015 0.001 TYR R 93 ARG 0.007 0.000 ARG R 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: R 54 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.6166 (m-10) REVERT: R 101 PHE cc_start: 0.4286 (OUTLIER) cc_final: 0.3996 (m-10) REVERT: R 139 ARG cc_start: 0.7365 (mtm-85) cc_final: 0.6758 (pmt-80) REVERT: R 162 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6075 (ptt) REVERT: R 293 TYR cc_start: 0.6405 (m-80) cc_final: 0.6183 (m-80) REVERT: A 184 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7683 (tt) REVERT: A 198 MET cc_start: 0.7782 (ttm) cc_final: 0.7571 (ttp) REVERT: A 274 PHE cc_start: 0.7222 (t80) cc_final: 0.6905 (t80) REVERT: B 19 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.6398 (tpp-160) REVERT: B 57 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8365 (mttt) REVERT: B 217 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7917 (pmt) REVERT: B 219 ARG cc_start: 0.7080 (mtt-85) cc_final: 0.6774 (mtm110) REVERT: B 322 ASP cc_start: 0.7861 (m-30) cc_final: 0.7638 (m-30) REVERT: G 21 MET cc_start: 0.6495 (mmp) cc_final: 0.6215 (tpp) REVERT: S 85 SER cc_start: 0.8146 (m) cc_final: 0.7804 (p) REVERT: S 87 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6742 (mtt90) REVERT: S 93 MET cc_start: 0.7897 (ttm) cc_final: 0.7693 (ttp) REVERT: S 109 ASP cc_start: 0.7814 (p0) cc_final: 0.7588 (p0) REVERT: S 142 SER cc_start: 0.6940 (p) cc_final: 0.6600 (m) REVERT: S 222 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7618 (pt0) outliers start: 33 outliers final: 20 residues processed: 146 average time/residue: 1.2548 time to fit residues: 195.5472 Evaluate side-chains 148 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 124 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 0.0870 chunk 104 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9307 Z= 0.151 Angle : 0.492 11.300 12613 Z= 0.254 Chirality : 0.040 0.137 1424 Planarity : 0.003 0.039 1588 Dihedral : 4.482 56.219 1262 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.02 % Favored : 97.89 % Rotamer: Outliers : 2.62 % Allowed : 17.44 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.12 (0.26), residues: 1139 helix: 1.73 (0.27), residues: 405 sheet: 0.56 (0.30), residues: 275 loop : 0.09 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.021 0.001 PHE R 110 TYR 0.014 0.001 TYR R 93 ARG 0.006 0.000 ARG R 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.082 Fit side-chains REVERT: R 36 MET cc_start: 0.5483 (tpp) cc_final: 0.3367 (tmm) REVERT: R 101 PHE cc_start: 0.4054 (OUTLIER) cc_final: 0.3694 (m-10) REVERT: R 114 TYR cc_start: 0.7690 (m-80) cc_final: 0.7399 (m-80) REVERT: R 139 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.6753 (pmt-80) REVERT: R 162 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.6006 (ptt) REVERT: R 293 TYR cc_start: 0.6381 (m-80) cc_final: 0.6106 (m-80) REVERT: A 184 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7685 (tt) REVERT: A 198 MET cc_start: 0.7761 (ttm) cc_final: 0.7550 (ttp) REVERT: A 274 PHE cc_start: 0.7262 (t80) cc_final: 0.6994 (t80) REVERT: B 19 ARG cc_start: 0.7274 (ttp-110) cc_final: 0.6378 (tpp-160) REVERT: B 217 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7896 (pmt) REVERT: B 219 ARG cc_start: 0.7082 (mtt-85) cc_final: 0.6769 (mtm110) REVERT: B 322 ASP cc_start: 0.7846 (m-30) cc_final: 0.7632 (m-30) REVERT: G 21 MET cc_start: 0.6456 (mmp) cc_final: 0.6182 (tpp) REVERT: S 85 SER cc_start: 0.8110 (m) cc_final: 0.7804 (p) REVERT: S 87 ARG cc_start: 0.7194 (mtt180) cc_final: 0.6767 (mtt90) REVERT: S 93 MET cc_start: 0.7839 (ttm) cc_final: 0.7629 (ttp) REVERT: S 109 ASP cc_start: 0.7757 (p0) cc_final: 0.7531 (p0) REVERT: S 142 SER cc_start: 0.6957 (p) cc_final: 0.6629 (m) REVERT: S 201 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7797 (t) outliers start: 26 outliers final: 13 residues processed: 142 average time/residue: 1.2609 time to fit residues: 192.0898 Evaluate side-chains 143 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 124 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 0.0060 chunk 65 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 176 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9307 Z= 0.190 Angle : 0.518 12.047 12613 Z= 0.267 Chirality : 0.041 0.143 1424 Planarity : 0.003 0.041 1588 Dihedral : 4.265 25.861 1260 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 2.62 % Allowed : 17.94 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.04 (0.26), residues: 1139 helix: 1.65 (0.27), residues: 405 sheet: 0.52 (0.29), residues: 293 loop : 0.03 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 154 HIS 0.003 0.001 HIS S 35 PHE 0.024 0.001 PHE R 110 TYR 0.014 0.001 TYR R 93 ARG 0.006 0.000 ARG R 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.095 Fit side-chains REVERT: R 36 MET cc_start: 0.5661 (tpp) cc_final: 0.3339 (tmm) REVERT: R 101 PHE cc_start: 0.4160 (OUTLIER) cc_final: 0.3774 (m-10) REVERT: R 139 ARG cc_start: 0.7324 (mtm-85) cc_final: 0.6707 (pmt-80) REVERT: R 162 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.6018 (ptt) REVERT: R 270 LEU cc_start: 0.7435 (mt) cc_final: 0.7166 (mt) REVERT: R 288 MET cc_start: 0.5036 (mmt) cc_final: 0.4794 (mmm) REVERT: R 293 TYR cc_start: 0.6453 (m-80) cc_final: 0.6170 (m-80) REVERT: A 184 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7707 (tt) REVERT: A 198 MET cc_start: 0.7788 (ttm) cc_final: 0.7576 (ttp) REVERT: A 274 PHE cc_start: 0.7279 (t80) cc_final: 0.6995 (t80) REVERT: B 19 ARG cc_start: 0.7302 (ttp-110) cc_final: 0.6372 (tpp-160) REVERT: B 217 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7858 (pmt) REVERT: B 219 ARG cc_start: 0.7090 (mtt-85) cc_final: 0.6757 (mtm110) REVERT: B 322 ASP cc_start: 0.7863 (m-30) cc_final: 0.7658 (m-30) REVERT: G 21 MET cc_start: 0.6407 (mmp) cc_final: 0.6154 (tpp) REVERT: S 6 GLU cc_start: 0.7617 (mp0) cc_final: 0.7415 (mt-10) REVERT: S 85 SER cc_start: 0.8113 (m) cc_final: 0.7804 (p) REVERT: S 87 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6759 (mtt90) REVERT: S 142 SER cc_start: 0.6950 (p) cc_final: 0.6609 (m) outliers start: 26 outliers final: 15 residues processed: 144 average time/residue: 1.2794 time to fit residues: 197.2016 Evaluate side-chains 147 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 124 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.0050 chunk 103 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 176 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9307 Z= 0.149 Angle : 0.504 12.427 12613 Z= 0.257 Chirality : 0.040 0.236 1424 Planarity : 0.003 0.039 1588 Dihedral : 4.166 25.676 1260 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.76 % Favored : 98.16 % Rotamer: Outliers : 2.02 % Allowed : 18.55 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.12 (0.26), residues: 1139 helix: 1.71 (0.27), residues: 406 sheet: 0.58 (0.29), residues: 277 loop : 0.06 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 154 HIS 0.002 0.001 HIS R 231 PHE 0.023 0.001 PHE R 110 TYR 0.012 0.001 TYR R 93 ARG 0.006 0.000 ARG R 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.102 Fit side-chains REVERT: R 36 MET cc_start: 0.5664 (tpp) cc_final: 0.3436 (tmm) REVERT: R 101 PHE cc_start: 0.4092 (OUTLIER) cc_final: 0.3709 (m-10) REVERT: R 139 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.6747 (pmt-80) REVERT: R 153 LEU cc_start: 0.6671 (pp) cc_final: 0.6453 (mm) REVERT: R 293 TYR cc_start: 0.6402 (m-80) cc_final: 0.6142 (m-80) REVERT: A 184 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7690 (tt) REVERT: A 198 MET cc_start: 0.7759 (ttm) cc_final: 0.7552 (ttp) REVERT: A 208 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7521 (ttp80) REVERT: B 19 ARG cc_start: 0.7295 (ttp-110) cc_final: 0.6384 (tpp-160) REVERT: B 217 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7887 (pmt) REVERT: B 219 ARG cc_start: 0.7080 (mtt-85) cc_final: 0.6761 (mtm110) REVERT: G 21 MET cc_start: 0.6394 (mmp) cc_final: 0.6153 (tpp) REVERT: S 85 SER cc_start: 0.8095 (m) cc_final: 0.7797 (p) REVERT: S 87 ARG cc_start: 0.7196 (mtt180) cc_final: 0.6758 (mtt90) REVERT: S 142 SER cc_start: 0.6846 (p) cc_final: 0.6506 (m) REVERT: S 201 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7789 (t) outliers start: 20 outliers final: 13 residues processed: 142 average time/residue: 1.2248 time to fit residues: 186.1611 Evaluate side-chains 142 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 124 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0270 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.121859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097094 restraints weight = 14322.938| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.74 r_work: 0.3235 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9307 Z= 0.169 Angle : 0.529 12.456 12613 Z= 0.267 Chirality : 0.041 0.145 1424 Planarity : 0.003 0.039 1588 Dihedral : 4.169 25.651 1260 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Rotamer: Outliers : 2.12 % Allowed : 18.75 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.10 (0.26), residues: 1139 helix: 1.72 (0.27), residues: 404 sheet: 0.51 (0.29), residues: 279 loop : 0.08 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 154 HIS 0.002 0.001 HIS B 142 PHE 0.037 0.001 PHE R 110 TYR 0.026 0.001 TYR R 93 ARG 0.006 0.000 ARG R 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3851.38 seconds wall clock time: 69 minutes 49.72 seconds (4189.72 seconds total)