Starting phenix.real_space_refine on Sun Apr 7 22:19:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2024/8f7r_28908_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2024/8f7r_28908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2024/8f7r_28908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2024/8f7r_28908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2024/8f7r_28908_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7r_28908/04_2024/8f7r_28908_updated.pdb" } resolution = 3.28 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= 0.002 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 98 5.16 5 C 7615 2.51 5 N 1900 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 97": "NH1" <-> "NH2" Residue "R ARG 181": "NH1" <-> "NH2" Residue "R ARG 213": "NH1" <-> "NH2" Residue "R ARG 260": "NH1" <-> "NH2" Residue "R ARG 265": "NH1" <-> "NH2" Residue "R ARG 275": "NH1" <-> "NH2" Residue "R ARG 278": "NH1" <-> "NH2" Residue "R ARG 282": "NH1" <-> "NH2" Residue "R ARG 347": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Residue "P PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M ARG 213": "NH1" <-> "NH2" Residue "M ARG 260": "NH1" <-> "NH2" Residue "M ARG 265": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M ARG 282": "NH1" <-> "NH2" Residue "M ARG 347": "NH1" <-> "NH2" Residue "M ARG 350": "NH1" <-> "NH2" Residue "Q PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11697 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PCIS': 1, 'TRANS': 2} Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2567 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain: "C" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 428 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {'NH2': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PCIS': 1, 'TRANS': 2} Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 130 Classifications: {'peptide': 17} Modifications used: {'COO': 1} Link IDs: {'TRANS': 16} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.76, per 1000 atoms: 0.58 Number of scatterers: 11697 At special positions: 0 Unit cell: (104.8, 108, 147.2, 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 98 16.00 O 2084 8.00 N 1900 7.00 C 7615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " 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: 4.63 Conformation dependent library (CDL) restraints added in 2.2 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 16 sheets defined 44.6% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'R' and resid 69 through 97 Processing helix chain 'R' and resid 104 through 121 Processing helix chain 'R' and resid 123 through 132 Processing helix chain 'R' and resid 139 through 172 removed outlier: 3.852A pdb=" N PHE R 154 " --> pdb=" O TYR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.889A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 207 removed outlier: 3.512A pdb=" N ALA R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 227 through 263 removed outlier: 5.538A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 271 through 307 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 314 through 338 removed outlier: 4.041A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 343 through 351 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.895A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 216 removed outlier: 4.706A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 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 309 Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.524A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.753A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'M' and resid 69 through 97 Processing helix chain 'M' and resid 104 through 121 Processing helix chain 'M' and resid 123 through 132 Processing helix chain 'M' and resid 139 through 172 removed outlier: 3.851A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 3.890A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 207 removed outlier: 3.512A pdb=" N ALA M 199 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 227 through 263 removed outlier: 5.538A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 271 through 307 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 314 through 338 removed outlier: 4.041A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 343 through 351 Processing helix chain 'F' and resid 339 through 351 Processing sheet with id= A, first strand: chain 'R' and resid 208 through 213 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.847A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.876A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.680A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.799A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.991A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.655A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.179A 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: 6.613A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.245A 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: 3.657A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.586A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.805A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER E 120 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 93 through 99 removed outlier: 3.527A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 147 through 149 removed outlier: 7.082A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 156 through 160 Processing sheet with id= O, first strand: chain 'E' and resid 227 through 232 removed outlier: 3.505A pdb=" N ILE E 190 " --> pdb=" O TRP E 177 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'M' and resid 208 through 213 598 hydrogen bonds defined for protein. 1746 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: 3.27 Time building geometry restraints manager: 5.04 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: 3511 1.34 - 1.46: 2327 1.46 - 1.58: 5996 1.58 - 1.70: 0 1.70 - 1.82: 145 Bond restraints: 11979 Sorted by residual: bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.34e+00 bond pdb=" C5 CLR R 404 " pdb=" C6 CLR R 404 " ideal model delta sigma weight residual 1.332 1.296 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C5 CLR M 405 " pdb=" C6 CLR M 405 " ideal model delta sigma weight residual 1.332 1.296 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" C10 CLR M 401 " pdb=" C9 CLR M 401 " ideal model delta sigma weight residual 1.551 1.518 0.033 2.00e-02 2.50e+03 2.64e+00 ... (remaining 11974 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.22: 308 106.22 - 113.18: 6678 113.18 - 120.14: 4172 120.14 - 127.10: 5019 127.10 - 134.06: 126 Bond angle restraints: 16303 Sorted by residual: angle pdb=" N PRO A 288 " pdb=" CA PRO A 288 " pdb=" CB PRO A 288 " ideal model delta sigma weight residual 103.44 109.80 -6.36 1.12e+00 7.97e-01 3.22e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 131.25 -9.71 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" CA PHE P 4 " pdb=" CB PHE P 4 " pdb=" CG PHE P 4 " ideal model delta sigma weight residual 113.80 116.70 -2.90 1.00e+00 1.00e+00 8.39e+00 angle pdb=" CA PHE Q 4 " pdb=" CB PHE Q 4 " pdb=" CG PHE Q 4 " ideal model delta sigma weight residual 113.80 116.68 -2.88 1.00e+00 1.00e+00 8.29e+00 ... (remaining 16298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.76: 6854 10.76 - 21.52: 596 21.52 - 32.28: 70 32.28 - 43.04: 33 43.04 - 53.81: 6 Dihedral angle restraints: 7559 sinusoidal: 3340 harmonic: 4219 Sorted by residual: 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 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA HIS B 266 " pdb=" C HIS B 266 " pdb=" N ASP B 267 " pdb=" CA ASP B 267 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 7556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1706 0.092 - 0.183: 162 0.183 - 0.275: 15 0.275 - 0.367: 11 0.367 - 0.459: 9 Chirality restraints: 1903 Sorted by residual: chirality pdb=" C14 CLR M 401 " pdb=" C13 CLR M 401 " pdb=" C15 CLR M 401 " pdb=" C8 CLR M 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C14 CLR R 405 " pdb=" C13 CLR R 405 " pdb=" C15 CLR R 405 " pdb=" C8 CLR R 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1900 not shown) Planarity restraints: 1964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO B 236 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 334 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO R 335 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 334 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO M 335 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 335 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO M 335 " 0.029 5.00e-02 4.00e+02 ... (remaining 1961 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2369 2.79 - 3.32: 10403 3.32 - 3.84: 19441 3.84 - 4.37: 21903 4.37 - 4.90: 39180 Nonbonded interactions: 93296 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.260 2.440 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.260 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.261 2.440 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.282 2.440 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.329 2.440 ... (remaining 93291 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 'M' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'Q' } 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: 3.240 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: 0.000 Extract box with map and model: 6.600 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.940 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11979 Z= 0.282 Angle : 0.839 9.710 16303 Z= 0.443 Chirality : 0.065 0.459 1903 Planarity : 0.006 0.064 1964 Dihedral : 8.210 53.806 4822 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -0.71 (0.19), residues: 1421 helix: 0.10 (0.16), residues: 653 sheet: 0.12 (0.31), residues: 276 loop : -1.47 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 111 HIS 0.006 0.001 HIS E 35 PHE 0.022 0.002 PHE R 349 TYR 0.022 0.002 TYR R 108 ARG 0.008 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 147 SER cc_start: 0.7480 (t) cc_final: 0.7261 (m) REVERT: R 195 ILE cc_start: 0.8729 (mt) cc_final: 0.8447 (mm) REVERT: R 200 ILE cc_start: 0.8162 (tp) cc_final: 0.7721 (tp) REVERT: R 212 TYR cc_start: 0.6749 (m-80) cc_final: 0.6296 (m-80) REVERT: A 305 CYS cc_start: 0.6977 (t) cc_final: 0.6498 (t) REVERT: B 198 LEU cc_start: 0.7505 (pp) cc_final: 0.7156 (mt) REVERT: C 18 GLN cc_start: 0.6833 (tp40) cc_final: 0.6279 (mm110) REVERT: E 80 PHE cc_start: 0.6714 (m-80) cc_final: 0.6347 (m-10) REVERT: E 220 LEU cc_start: 0.8039 (tp) cc_final: 0.7827 (tt) REVERT: M 328 TYR cc_start: 0.7240 (m-80) cc_final: 0.6413 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2805 time to fit residues: 111.1513 Evaluate side-chains 190 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 7.9990 chunk 106 optimal weight: 0.0370 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 chunk 127 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN A 188 HIS B 88 ASN B 91 HIS B 183 HIS B 266 HIS C 44 HIS E 168 HIS E 184 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 321 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11979 Z= 0.157 Angle : 0.494 5.370 16303 Z= 0.256 Chirality : 0.039 0.140 1903 Planarity : 0.004 0.051 1964 Dihedral : 5.338 41.899 2215 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.43 % Allowed : 6.03 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 0.84 (0.21), residues: 1421 helix: 1.80 (0.18), residues: 657 sheet: 0.23 (0.31), residues: 277 loop : -0.95 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.010 0.001 HIS B 225 PHE 0.023 0.001 PHE E 27 TYR 0.016 0.001 TYR A 296 ARG 0.007 0.001 ARG E 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7748 (tpp) cc_final: 0.7472 (tpt) REVERT: R 188 ILE cc_start: 0.8053 (mt) cc_final: 0.7794 (mp) REVERT: R 195 ILE cc_start: 0.8646 (mt) cc_final: 0.7968 (mm) REVERT: R 198 SER cc_start: 0.8119 (t) cc_final: 0.7691 (p) REVERT: R 212 TYR cc_start: 0.6713 (m-80) cc_final: 0.6182 (m-80) REVERT: A 197 LYS cc_start: 0.8157 (mttt) cc_final: 0.7938 (mmtm) REVERT: A 305 CYS cc_start: 0.7245 (t) cc_final: 0.6781 (t) REVERT: A 308 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: C 18 GLN cc_start: 0.7000 (tp40) cc_final: 0.6411 (mm110) REVERT: E 18 ARG cc_start: 0.3958 (ttt180) cc_final: 0.3723 (ttt180) REVERT: E 80 PHE cc_start: 0.6562 (m-80) cc_final: 0.6080 (m-10) REVERT: E 161 ARG cc_start: 0.6806 (mmm160) cc_final: 0.6360 (ttm-80) REVERT: E 220 LEU cc_start: 0.8067 (tp) cc_final: 0.7867 (tt) REVERT: M 332 CYS cc_start: 0.6472 (t) cc_final: 0.6030 (p) outliers start: 18 outliers final: 9 residues processed: 230 average time/residue: 0.2787 time to fit residues: 88.4967 Evaluate side-chains 200 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain M residue 86 PHE Chi-restraints excluded: chain M residue 146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 299 HIS R 334 ASN B 230 ASN E 82 GLN ** M 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11979 Z= 0.298 Angle : 0.592 6.433 16303 Z= 0.307 Chirality : 0.042 0.143 1903 Planarity : 0.004 0.046 1964 Dihedral : 5.428 33.593 2215 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.98 % Allowed : 7.85 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.11 (0.22), residues: 1421 helix: 1.94 (0.19), residues: 660 sheet: 0.47 (0.32), residues: 286 loop : -0.79 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 332 HIS 0.010 0.002 HIS B 54 PHE 0.021 0.002 PHE M 291 TYR 0.022 0.002 TYR R 301 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7824 (tpp) cc_final: 0.7232 (tpt) REVERT: R 102 LYS cc_start: 0.7526 (ptpt) cc_final: 0.7098 (mmtm) REVERT: R 195 ILE cc_start: 0.8774 (mt) cc_final: 0.8043 (mm) REVERT: R 198 SER cc_start: 0.8672 (t) cc_final: 0.8195 (p) REVERT: R 212 TYR cc_start: 0.6581 (m-80) cc_final: 0.6103 (m-80) REVERT: R 340 PHE cc_start: 0.7379 (m-10) cc_final: 0.6220 (t80) REVERT: A 197 LYS cc_start: 0.8293 (mttt) cc_final: 0.7976 (mmtm) REVERT: A 305 CYS cc_start: 0.7277 (t) cc_final: 0.6967 (t) REVERT: A 308 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: B 82 TRP cc_start: 0.7468 (OUTLIER) cc_final: 0.6024 (m-10) REVERT: B 172 GLU cc_start: 0.7079 (tp30) cc_final: 0.6728 (tm-30) REVERT: B 239 ASN cc_start: 0.7405 (m-40) cc_final: 0.6956 (p0) REVERT: E 18 ARG cc_start: 0.3989 (ttt180) cc_final: 0.3785 (ttt180) REVERT: E 141 MET cc_start: 0.7416 (mmm) cc_final: 0.6997 (mmm) REVERT: E 161 ARG cc_start: 0.6946 (mmm160) cc_final: 0.6724 (ttp-110) REVERT: E 221 GLU cc_start: 0.7239 (tt0) cc_final: 0.7031 (tt0) outliers start: 25 outliers final: 16 residues processed: 233 average time/residue: 0.2245 time to fit residues: 71.9160 Evaluate side-chains 200 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 317 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 0.0570 chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 321 HIS B 176 GLN C 18 GLN ** M 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 299 HIS M 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11979 Z= 0.154 Angle : 0.484 7.781 16303 Z= 0.247 Chirality : 0.039 0.132 1903 Planarity : 0.003 0.042 1964 Dihedral : 4.935 33.799 2215 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.74 % Allowed : 11.50 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.55 (0.22), residues: 1421 helix: 2.44 (0.20), residues: 642 sheet: 0.43 (0.32), residues: 289 loop : -0.50 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 320 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.001 PHE E 27 TYR 0.011 0.001 TYR M 151 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7795 (tpp) cc_final: 0.7212 (tpt) REVERT: R 102 LYS cc_start: 0.7429 (ptpt) cc_final: 0.7047 (mmtm) REVERT: R 195 ILE cc_start: 0.8690 (mt) cc_final: 0.7951 (mm) REVERT: R 198 SER cc_start: 0.8592 (t) cc_final: 0.8053 (p) REVERT: R 212 TYR cc_start: 0.6514 (m-80) cc_final: 0.6030 (m-80) REVERT: R 283 MET cc_start: 0.6462 (tpp) cc_final: 0.6140 (mtt) REVERT: R 340 PHE cc_start: 0.7278 (m-10) cc_final: 0.6165 (t80) REVERT: A 305 CYS cc_start: 0.7320 (t) cc_final: 0.6612 (t) REVERT: A 308 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: B 172 GLU cc_start: 0.6983 (tp30) cc_final: 0.6519 (tm-30) REVERT: B 239 ASN cc_start: 0.7414 (m-40) cc_final: 0.7100 (p0) REVERT: E 18 ARG cc_start: 0.3840 (ttt180) cc_final: 0.3597 (ttt180) REVERT: E 55 SER cc_start: 0.7542 (m) cc_final: 0.6982 (p) REVERT: E 141 MET cc_start: 0.7410 (mmm) cc_final: 0.7122 (mmm) outliers start: 22 outliers final: 16 residues processed: 205 average time/residue: 0.2561 time to fit residues: 73.3453 Evaluate side-chains 198 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 176 GLN B 259 GLN ** M 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11979 Z= 0.326 Angle : 0.582 7.090 16303 Z= 0.300 Chirality : 0.042 0.146 1903 Planarity : 0.004 0.041 1964 Dihedral : 5.436 33.374 2215 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.93 % Allowed : 11.90 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.18 (0.22), residues: 1421 helix: 2.09 (0.20), residues: 646 sheet: 0.21 (0.31), residues: 282 loop : -0.61 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 82 HIS 0.007 0.002 HIS B 54 PHE 0.022 0.002 PHE B 278 TYR 0.022 0.002 TYR R 301 ARG 0.012 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7830 (tpp) cc_final: 0.7475 (tpt) REVERT: R 100 LYS cc_start: 0.6832 (mttt) cc_final: 0.6514 (mptt) REVERT: R 102 LYS cc_start: 0.7730 (ptpt) cc_final: 0.7140 (mmtm) REVERT: R 195 ILE cc_start: 0.8754 (mt) cc_final: 0.8001 (mm) REVERT: R 198 SER cc_start: 0.8766 (t) cc_final: 0.8234 (p) REVERT: R 212 TYR cc_start: 0.6422 (m-80) cc_final: 0.5907 (m-80) REVERT: A 197 LYS cc_start: 0.8198 (mttm) cc_final: 0.7914 (mtpt) REVERT: A 305 CYS cc_start: 0.7187 (t) cc_final: 0.6790 (t) REVERT: A 308 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: B 82 TRP cc_start: 0.7450 (OUTLIER) cc_final: 0.6623 (m-10) REVERT: B 239 ASN cc_start: 0.7660 (m-40) cc_final: 0.7253 (p0) REVERT: B 292 PHE cc_start: 0.7553 (m-80) cc_final: 0.7228 (m-10) REVERT: E 18 ARG cc_start: 0.4102 (ttt180) cc_final: 0.3901 (ttt180) REVERT: E 141 MET cc_start: 0.7577 (mmm) cc_final: 0.7225 (mmm) REVERT: E 193 MET cc_start: 0.6182 (mmm) cc_final: 0.5968 (ttp) REVERT: M 245 MET cc_start: 0.6127 (mmp) cc_final: 0.5857 (ttm) outliers start: 37 outliers final: 25 residues processed: 214 average time/residue: 0.2719 time to fit residues: 80.5114 Evaluate side-chains 196 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 0.1980 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 75 GLN B 259 GLN E 39 GLN E 180 GLN ** M 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11979 Z= 0.174 Angle : 0.493 7.081 16303 Z= 0.253 Chirality : 0.039 0.136 1903 Planarity : 0.003 0.039 1964 Dihedral : 5.018 32.559 2215 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.17 % Allowed : 12.77 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.45 (0.22), residues: 1421 helix: 2.35 (0.20), residues: 646 sheet: 0.25 (0.31), residues: 280 loop : -0.45 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.001 PHE E 27 TYR 0.010 0.001 TYR R 301 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7838 (tpp) cc_final: 0.7436 (tpt) REVERT: R 198 SER cc_start: 0.8689 (t) cc_final: 0.8146 (p) REVERT: R 212 TYR cc_start: 0.6327 (m-80) cc_final: 0.5834 (m-80) REVERT: R 283 MET cc_start: 0.6479 (tpp) cc_final: 0.6266 (mtt) REVERT: A 33 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6759 (mt-10) REVERT: A 197 LYS cc_start: 0.8226 (mttm) cc_final: 0.7817 (mtpt) REVERT: A 305 CYS cc_start: 0.7179 (t) cc_final: 0.6817 (t) REVERT: A 308 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: B 82 TRP cc_start: 0.7361 (OUTLIER) cc_final: 0.6575 (m-10) REVERT: B 239 ASN cc_start: 0.7649 (m-40) cc_final: 0.7325 (p0) REVERT: B 292 PHE cc_start: 0.7278 (m-80) cc_final: 0.6940 (m-10) REVERT: E 18 ARG cc_start: 0.3953 (ttt180) cc_final: 0.3718 (ttt180) REVERT: E 141 MET cc_start: 0.7541 (mmm) cc_final: 0.7208 (mmm) REVERT: M 92 MET cc_start: 0.6174 (mmt) cc_final: 0.5868 (mmt) outliers start: 40 outliers final: 26 residues processed: 212 average time/residue: 0.2566 time to fit residues: 76.8659 Evaluate side-chains 199 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.0670 chunk 83 optimal weight: 7.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 306 GLN E 39 GLN ** M 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11979 Z= 0.160 Angle : 0.483 7.803 16303 Z= 0.249 Chirality : 0.038 0.138 1903 Planarity : 0.003 0.038 1964 Dihedral : 4.890 31.895 2215 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.70 % Allowed : 13.40 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.57 (0.22), residues: 1421 helix: 2.44 (0.20), residues: 646 sheet: 0.34 (0.31), residues: 284 loop : -0.41 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.021 0.001 PHE A 334 TYR 0.012 0.001 TYR E 95 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.7837 (tpp) cc_final: 0.7453 (tpt) REVERT: R 195 ILE cc_start: 0.8786 (mt) cc_final: 0.8039 (mm) REVERT: R 198 SER cc_start: 0.8658 (t) cc_final: 0.8110 (p) REVERT: R 212 TYR cc_start: 0.6293 (m-80) cc_final: 0.5887 (m-80) REVERT: R 283 MET cc_start: 0.6451 (tpp) cc_final: 0.6240 (mtt) REVERT: R 340 PHE cc_start: 0.7442 (m-10) cc_final: 0.7019 (m-10) REVERT: A 305 CYS cc_start: 0.7203 (t) cc_final: 0.6825 (t) REVERT: A 308 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: B 82 TRP cc_start: 0.7354 (OUTLIER) cc_final: 0.6525 (m-10) REVERT: B 239 ASN cc_start: 0.7655 (m-40) cc_final: 0.7372 (p0) REVERT: B 262 MET cc_start: 0.6944 (mmm) cc_final: 0.6577 (mmm) REVERT: B 292 PHE cc_start: 0.7260 (m-80) cc_final: 0.6936 (m-10) REVERT: E 18 ARG cc_start: 0.3855 (ttt180) cc_final: 0.3613 (ttt180) REVERT: E 141 MET cc_start: 0.7534 (mmm) cc_final: 0.7192 (mmm) REVERT: M 92 MET cc_start: 0.6217 (mmt) cc_final: 0.5955 (mmt) REVERT: M 328 TYR cc_start: 0.7739 (m-80) cc_final: 0.6558 (m-80) outliers start: 34 outliers final: 26 residues processed: 210 average time/residue: 0.2624 time to fit residues: 76.8625 Evaluate side-chains 201 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 334 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN E 39 GLN M 173 HIS ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11979 Z= 0.293 Angle : 0.563 7.568 16303 Z= 0.290 Chirality : 0.041 0.145 1903 Planarity : 0.004 0.047 1964 Dihedral : 5.235 38.103 2215 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.57 % Allowed : 12.61 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.22), residues: 1421 helix: 2.17 (0.20), residues: 655 sheet: 0.19 (0.31), residues: 285 loop : -0.37 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 47 HIS 0.006 0.002 HIS B 142 PHE 0.017 0.002 PHE B 278 TYR 0.017 0.002 TYR R 301 ARG 0.007 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 180 time to evaluate : 1.448 Fit side-chains REVERT: R 74 MET cc_start: 0.7858 (tpp) cc_final: 0.7494 (tpt) REVERT: R 195 ILE cc_start: 0.8810 (mt) cc_final: 0.8070 (mm) REVERT: R 198 SER cc_start: 0.8733 (t) cc_final: 0.8194 (p) REVERT: R 212 TYR cc_start: 0.6286 (m-80) cc_final: 0.5886 (m-80) REVERT: A 33 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6967 (mt-10) REVERT: A 305 CYS cc_start: 0.7225 (t) cc_final: 0.6836 (t) REVERT: A 308 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6497 (mp0) REVERT: B 82 TRP cc_start: 0.7512 (OUTLIER) cc_final: 0.6815 (m-10) REVERT: B 239 ASN cc_start: 0.7666 (m-40) cc_final: 0.7354 (p0) REVERT: B 262 MET cc_start: 0.6845 (mmm) cc_final: 0.6511 (mmm) REVERT: E 18 ARG cc_start: 0.4198 (ttt180) cc_final: 0.3965 (ttt180) REVERT: E 141 MET cc_start: 0.7533 (mmm) cc_final: 0.7188 (mmm) outliers start: 45 outliers final: 36 residues processed: 215 average time/residue: 0.2669 time to fit residues: 80.0949 Evaluate side-chains 210 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 334 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 75 GLN E 39 GLN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11979 Z= 0.205 Angle : 0.526 11.236 16303 Z= 0.271 Chirality : 0.040 0.267 1903 Planarity : 0.004 0.040 1964 Dihedral : 5.123 38.461 2215 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.09 % Allowed : 13.24 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.38 (0.22), residues: 1421 helix: 2.21 (0.20), residues: 649 sheet: 0.17 (0.31), residues: 285 loop : -0.36 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 47 HIS 0.004 0.001 HIS B 142 PHE 0.023 0.001 PHE E 213 TYR 0.012 0.001 TYR R 301 ARG 0.009 0.001 ARG E 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7896 (tpp) cc_final: 0.7511 (tpt) REVERT: R 195 ILE cc_start: 0.8790 (mt) cc_final: 0.8053 (mm) REVERT: R 198 SER cc_start: 0.8697 (t) cc_final: 0.8146 (p) REVERT: R 212 TYR cc_start: 0.6247 (m-80) cc_final: 0.5854 (m-80) REVERT: A 33 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6947 (mt-10) REVERT: A 305 CYS cc_start: 0.7201 (t) cc_final: 0.6820 (t) REVERT: A 308 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: B 82 TRP cc_start: 0.7464 (OUTLIER) cc_final: 0.6764 (m-10) REVERT: B 239 ASN cc_start: 0.7680 (m-40) cc_final: 0.7395 (p0) REVERT: B 262 MET cc_start: 0.6817 (mmm) cc_final: 0.6511 (mmm) REVERT: E 18 ARG cc_start: 0.4118 (ttt180) cc_final: 0.3907 (ttt180) REVERT: E 141 MET cc_start: 0.7563 (mmm) cc_final: 0.7209 (mmm) REVERT: M 328 TYR cc_start: 0.7789 (m-80) cc_final: 0.6603 (m-80) outliers start: 39 outliers final: 31 residues processed: 212 average time/residue: 0.2644 time to fit residues: 78.9136 Evaluate side-chains 210 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain M residue 334 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN E 39 GLN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11979 Z= 0.309 Angle : 0.585 9.412 16303 Z= 0.300 Chirality : 0.042 0.253 1903 Planarity : 0.004 0.040 1964 Dihedral : 5.452 43.445 2215 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.09 % Allowed : 13.56 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.07 (0.22), residues: 1421 helix: 1.89 (0.20), residues: 659 sheet: 0.06 (0.30), residues: 281 loop : -0.49 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 47 HIS 0.005 0.001 HIS B 62 PHE 0.020 0.002 PHE E 213 TYR 0.018 0.002 TYR R 301 ARG 0.010 0.001 ARG E 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.7910 (tpp) cc_final: 0.7550 (tpt) REVERT: R 198 SER cc_start: 0.8743 (t) cc_final: 0.8208 (p) REVERT: R 212 TYR cc_start: 0.6348 (m-80) cc_final: 0.5967 (m-80) REVERT: A 277 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6497 (ttmm) REVERT: A 305 CYS cc_start: 0.7181 (t) cc_final: 0.6799 (t) REVERT: A 308 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: B 82 TRP cc_start: 0.7520 (OUTLIER) cc_final: 0.6893 (m-10) REVERT: B 239 ASN cc_start: 0.7658 (m-40) cc_final: 0.7364 (p0) REVERT: B 262 MET cc_start: 0.6722 (mmm) cc_final: 0.6456 (mmm) REVERT: E 46 GLU cc_start: 0.6519 (tt0) cc_final: 0.6217 (pt0) REVERT: E 141 MET cc_start: 0.7517 (mmm) cc_final: 0.7149 (mmm) REVERT: M 124 PRO cc_start: 0.6319 (Cg_exo) cc_final: 0.6050 (Cg_endo) REVERT: M 220 THR cc_start: 0.8012 (t) cc_final: 0.7746 (p) REVERT: M 245 MET cc_start: 0.6187 (mmp) cc_final: 0.5877 (ttm) outliers start: 39 outliers final: 33 residues processed: 213 average time/residue: 0.2675 time to fit residues: 79.3562 Evaluate side-chains 210 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 179 ASP Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 317 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 114 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 306 GLN B 75 GLN E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142529 restraints weight = 13302.852| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.97 r_work: 0.3573 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11979 Z= 0.213 Angle : 0.542 10.207 16303 Z= 0.280 Chirality : 0.040 0.230 1903 Planarity : 0.004 0.040 1964 Dihedral : 5.263 44.039 2215 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.17 % Allowed : 14.20 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.23 (0.22), residues: 1421 helix: 2.13 (0.20), residues: 645 sheet: 0.11 (0.30), residues: 279 loop : -0.47 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 47 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.001 PHE E 213 TYR 0.013 0.001 TYR A 302 ARG 0.008 0.001 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.52 seconds wall clock time: 56 minutes 34.89 seconds (3394.89 seconds total)