Starting phenix.real_space_refine on Wed Feb 14 05:52:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/02_2024/8id3_35356_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/02_2024/8id3_35356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/02_2024/8id3_35356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/02_2024/8id3_35356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/02_2024/8id3_35356_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/02_2024/8id3_35356_updated.pdb" } resolution = 3.1 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= 0.012 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 58 5.16 5 C 5585 2.51 5 N 1492 2.21 5 O 1607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8742 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2566 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "S" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1752 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 432 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1762 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "R" Number of atoms: 2230 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 292, 2219 Unusual residues: {'7NR': 1} Classifications: {'peptide': 291, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 11, 'TRANS': 279, None: 1} Not linked: pdbres="LEU R 325 " pdbres="7NR R 401 " Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 70 Conformer: "B" Number of residues, atoms: 292, 2219 Unusual residues: {'7NR': 1} Classifications: {'peptide': 291, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 11, 'TRANS': 279, None: 1} Not linked: pdbres="LEU R 325 " pdbres="7NR R 401 " Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 70 bond proxies already assigned to first conformer: 2254 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG R 261 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG R 261 " occ=0.50 Time building chain proxies: 6.50, per 1000 atoms: 0.74 Number of scatterers: 8742 At special positions: 0 Unit cell: (107.484, 126.75, 117.624, 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 58 16.00 O 1607 8.00 N 1492 7.00 C 5585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " 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: 3.21 Conformation dependent library (CDL) restraints added in 2.2 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 32.3% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.225A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) 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 222 through 224 No H-bonds generated for 'chain 'S' and resid 222 through 224' Processing helix chain 'Y' and resid 7 through 22 Processing helix chain 'Y' and resid 30 through 43 Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 46 through 52 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 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.911A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (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: 4.057A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'R' and resid 38 through 67 Processing helix chain 'R' and resid 77 through 98 removed outlier: 3.511A pdb=" N LEU R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 111 through 141 removed outlier: 4.236A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 169 removed outlier: 3.783A pdb=" N ALA R 160 " --> pdb=" O ALA R 156 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU R 161 " --> pdb=" O VAL R 157 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA R 167 " --> pdb=" O TRP R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 175 removed outlier: 4.359A pdb=" N VAL R 175 " --> pdb=" O PRO R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 215 removed outlier: 4.407A pdb=" N ILE R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP R 208 " --> pdb=" O GLU R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 244 removed outlier: 3.545A pdb=" N ARG R 240 " --> pdb=" O ALA R 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 263 removed outlier: 3.877A pdb=" N SER R 256 " --> pdb=" O GLN R 252 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE R 260 " --> pdb=" O SER R 256 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N AARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 293 removed outlier: 3.662A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) Proline residue: R 279 - end of helix removed outlier: 3.945A pdb=" N ASN R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 322 removed outlier: 3.567A pdb=" N ALA R 312 " --> pdb=" O ALA R 308 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 4.622A pdb=" N ASN R 322 " --> pdb=" O PRO R 318 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.819A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.864A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.631A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 249 through 252 Processing sheet with id= F, first strand: chain 'B' and resid 276 through 278 removed outlier: 5.614A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.656A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.758A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 93 through 99 removed outlier: 3.599A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 141 through 143 removed outlier: 3.694A pdb=" N ALA S 212 " --> pdb=" O SER S 209 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 244 through 246 removed outlier: 3.636A pdb=" N ILE S 190 " --> pdb=" O TRP S 177 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.871A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1009 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: 2.30 Time building geometry restraints manager: 3.47 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: 2808 1.34 - 1.46: 1586 1.46 - 1.57: 4438 1.57 - 1.69: 1 1.69 - 1.81: 84 Bond restraints: 8917 Sorted by residual: bond pdb=" C LEU A 353 " pdb=" N PHE A 354 " ideal model delta sigma weight residual 1.329 1.296 0.033 1.40e-02 5.10e+03 5.65e+00 bond pdb=" N ARG R 71 " pdb=" CA ARG R 71 " ideal model delta sigma weight residual 1.458 1.485 -0.028 1.17e-02 7.31e+03 5.54e+00 bond pdb=" N ARG R 70 " pdb=" CA ARG R 70 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.44e+00 bond pdb=" N ARG R 69 " pdb=" CA ARG R 69 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.10e+00 bond pdb=" N ARG R 68 " pdb=" CA ARG R 68 " ideal model delta sigma weight residual 1.464 1.489 -0.025 1.30e-02 5.92e+03 3.78e+00 ... (remaining 8912 not shown) Histogram of bond angle deviations from ideal: 95.22 - 104.53: 102 104.53 - 113.84: 5158 113.84 - 123.15: 6312 123.15 - 132.47: 508 132.47 - 141.78: 22 Bond angle restraints: 12102 Sorted by residual: angle pdb=" CD ARG R 254 " pdb=" NE ARG R 254 " pdb=" CZ ARG R 254 " ideal model delta sigma weight residual 124.40 97.41 26.99 1.40e+00 5.10e-01 3.72e+02 angle pdb=" CA ASP R 259 " pdb=" CB ASP R 259 " pdb=" CG ASP R 259 " ideal model delta sigma weight residual 112.60 103.66 8.94 1.00e+00 1.00e+00 7.99e+01 angle pdb=" CA GLN R 258 " pdb=" CB GLN R 258 " pdb=" CG GLN R 258 " ideal model delta sigma weight residual 114.10 130.28 -16.18 2.00e+00 2.50e-01 6.55e+01 angle pdb=" CA LEU R 86 " pdb=" CB LEU R 86 " pdb=" CG LEU R 86 " ideal model delta sigma weight residual 116.30 141.78 -25.48 3.50e+00 8.16e-02 5.30e+01 angle pdb=" N VAL R 109 " pdb=" CA VAL R 109 " pdb=" C VAL R 109 " ideal model delta sigma weight residual 113.71 107.13 6.58 9.50e-01 1.11e+00 4.80e+01 ... (remaining 12097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4811 17.63 - 35.25: 374 35.25 - 52.88: 63 52.88 - 70.50: 18 70.50 - 88.13: 7 Dihedral angle restraints: 5273 sinusoidal: 1963 harmonic: 3310 Sorted by residual: dihedral pdb=" CD ARG R 69 " pdb=" NE ARG R 69 " pdb=" CZ ARG R 69 " pdb=" NH1 ARG R 69 " ideal model delta sinusoidal sigma weight residual 0.00 75.86 -75.86 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS S 160 " pdb=" SG CYS S 160 " pdb=" SG CYS S 230 " pdb=" CB CYS S 230 " ideal model delta sinusoidal sigma weight residual 93.00 158.16 -65.16 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CA HIS R 142 " pdb=" C HIS R 142 " pdb=" N LEU R 143 " pdb=" CA LEU R 143 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1223 0.066 - 0.132: 178 0.132 - 0.197: 11 0.197 - 0.263: 0 0.263 - 0.329: 2 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE R 89 " pdb=" CA ILE R 89 " pdb=" CG1 ILE R 89 " pdb=" CG2 ILE R 89 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C04 7NR R 401 " pdb=" C05 7NR R 401 " pdb=" C06 7NR R 401 " pdb=" O01 7NR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.76 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ARG R 71 " pdb=" N ARG R 71 " pdb=" C ARG R 71 " pdb=" CB ARG R 71 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 1411 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 69 " 1.062 9.50e-02 1.11e+02 4.76e-01 1.37e+02 pdb=" NE ARG R 69 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG R 69 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG R 69 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG R 69 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 115 " 0.082 2.00e-02 2.50e+03 5.02e-02 4.41e+01 pdb=" CG PHE R 115 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 PHE R 115 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE R 115 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE R 115 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE R 115 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE R 115 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 68 " -0.569 9.50e-02 1.11e+02 2.55e-01 3.98e+01 pdb=" NE ARG R 68 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG R 68 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG R 68 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 68 " -0.018 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 769 2.74 - 3.28: 8431 3.28 - 3.82: 13931 3.82 - 4.36: 16578 4.36 - 4.90: 29618 Nonbonded interactions: 69327 Sorted by model distance: nonbonded pdb=" CD ARG R 254 " pdb=" NH1 ARG R 254 " model vdw 2.199 2.816 nonbonded pdb=" O ASN A 347 " pdb=" OD1 ASP A 350 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP B 228 " pdb=" NZ LYS A 209 " model vdw 2.277 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.278 2.440 nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.300 2.520 ... (remaining 69322 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=0.50 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: 0.340 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: 2.050 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.600 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.005 0.094 8917 Z= 0.294 Angle : 0.854 26.993 12102 Z= 0.505 Chirality : 0.048 0.329 1414 Planarity : 0.015 0.476 1520 Dihedral : 13.646 88.129 3128 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.76 % Allowed : 0.33 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.42 (0.24), residues: 1126 helix: -0.23 (0.27), residues: 372 sheet: -0.72 (0.30), residues: 289 loop : -1.57 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 104 HIS 0.004 0.001 HIS B 91 PHE 0.082 0.003 PHE R 115 TYR 0.013 0.001 TYR R 165 ARG 0.008 0.000 ARG S 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 1.024 Fit side-chains REVERT: B 290 ASP cc_start: 0.7274 (m-30) cc_final: 0.6962 (m-30) REVERT: A 229 ASP cc_start: 0.8172 (t70) cc_final: 0.7757 (t70) REVERT: A 245 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 298 GLU cc_start: 0.7887 (pt0) cc_final: 0.7473 (pt0) REVERT: A 354 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.7052 (t80) outliers start: 6 outliers final: 1 residues processed: 161 average time/residue: 0.2409 time to fit residues: 51.8458 Evaluate side-chains 141 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 0.0000 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 8917 Z= 0.156 Angle : 0.519 7.093 12102 Z= 0.271 Chirality : 0.041 0.137 1414 Planarity : 0.004 0.049 1520 Dihedral : 5.364 56.382 1250 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.52 % Allowed : 6.51 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.68 (0.25), residues: 1126 helix: 0.69 (0.28), residues: 365 sheet: -0.43 (0.30), residues: 289 loop : -1.32 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 207 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE R 177 TYR 0.012 0.001 TYR R 165 ARG 0.006 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.044 Fit side-chains REVERT: B 259 GLN cc_start: 0.7357 (tt0) cc_final: 0.6524 (mt0) REVERT: B 290 ASP cc_start: 0.7283 (m-30) cc_final: 0.7058 (m-30) REVERT: B 294 CYS cc_start: 0.7571 (m) cc_final: 0.7275 (t) REVERT: A 229 ASP cc_start: 0.7959 (t70) cc_final: 0.7398 (t70) REVERT: A 354 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6826 (t80) REVERT: R 67 ARG cc_start: 0.6807 (tpp80) cc_final: 0.6573 (tpp80) REVERT: R 70 ARG cc_start: 0.6597 (ptt-90) cc_final: 0.5399 (mmp-170) REVERT: R 178 ARG cc_start: 0.7098 (mmt90) cc_final: 0.6839 (mmm160) outliers start: 13 outliers final: 8 residues processed: 151 average time/residue: 0.2666 time to fit residues: 52.8300 Evaluate side-chains 144 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8917 Z= 0.166 Angle : 0.509 7.335 12102 Z= 0.264 Chirality : 0.041 0.140 1414 Planarity : 0.003 0.044 1520 Dihedral : 4.778 57.371 1248 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.41 % Allowed : 9.22 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.38 (0.25), residues: 1126 helix: 0.99 (0.29), residues: 370 sheet: -0.26 (0.30), residues: 293 loop : -1.22 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 207 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE S 68 TYR 0.020 0.001 TYR R 165 ARG 0.004 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.065 Fit side-chains REVERT: B 259 GLN cc_start: 0.7419 (tt0) cc_final: 0.6552 (mt0) REVERT: B 294 CYS cc_start: 0.7522 (m) cc_final: 0.7249 (t) REVERT: A 229 ASP cc_start: 0.7871 (t70) cc_final: 0.7251 (t70) REVERT: A 354 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6684 (t80) REVERT: R 67 ARG cc_start: 0.6801 (tpp80) cc_final: 0.6560 (tpp80) REVERT: R 70 ARG cc_start: 0.6430 (ptt-90) cc_final: 0.5330 (mmp-170) REVERT: R 178 ARG cc_start: 0.7072 (mmt90) cc_final: 0.6782 (mmm160) outliers start: 12 outliers final: 8 residues processed: 146 average time/residue: 0.2479 time to fit residues: 48.4836 Evaluate side-chains 144 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 0.0370 chunk 96 optimal weight: 0.0570 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 60 optimal weight: 8.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8917 Z= 0.118 Angle : 0.472 7.317 12102 Z= 0.243 Chirality : 0.040 0.128 1414 Planarity : 0.003 0.043 1520 Dihedral : 4.436 56.740 1248 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.19 % Allowed : 10.41 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.15 (0.25), residues: 1126 helix: 1.16 (0.29), residues: 371 sheet: -0.02 (0.30), residues: 285 loop : -1.14 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE S 68 TYR 0.015 0.001 TYR R 165 ARG 0.003 0.000 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.021 Fit side-chains REVERT: B 259 GLN cc_start: 0.7354 (tt0) cc_final: 0.6531 (mt0) REVERT: A 229 ASP cc_start: 0.8015 (t70) cc_final: 0.7455 (t70) REVERT: A 354 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6656 (t80) REVERT: R 70 ARG cc_start: 0.6496 (ptt-90) cc_final: 0.5468 (mmp-170) outliers start: 10 outliers final: 6 residues processed: 147 average time/residue: 0.2259 time to fit residues: 45.0996 Evaluate side-chains 139 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8917 Z= 0.426 Angle : 0.639 8.051 12102 Z= 0.335 Chirality : 0.046 0.155 1414 Planarity : 0.004 0.050 1520 Dihedral : 5.169 59.565 1248 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.39 % Allowed : 11.17 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.46 (0.25), residues: 1126 helix: 0.76 (0.28), residues: 374 sheet: -0.19 (0.30), residues: 297 loop : -1.22 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 36 HIS 0.008 0.001 HIS B 91 PHE 0.018 0.002 PHE B 234 TYR 0.019 0.002 TYR B 59 ARG 0.005 0.001 ARG R 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.043 Fit side-chains REVERT: A 229 ASP cc_start: 0.7888 (t70) cc_final: 0.7188 (t70) REVERT: A 276 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7525 (mp0) outliers start: 21 outliers final: 15 residues processed: 141 average time/residue: 0.2444 time to fit residues: 45.9014 Evaluate side-chains 142 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8917 Z= 0.145 Angle : 0.515 15.791 12102 Z= 0.262 Chirality : 0.041 0.131 1414 Planarity : 0.003 0.047 1520 Dihedral : 4.801 57.724 1248 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.95 % Allowed : 13.23 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.12 (0.26), residues: 1126 helix: 1.20 (0.29), residues: 373 sheet: -0.01 (0.30), residues: 295 loop : -1.16 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.000 HIS S 35 PHE 0.013 0.001 PHE R 216 TYR 0.010 0.001 TYR R 165 ARG 0.006 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8033 (t70) cc_final: 0.7372 (t70) REVERT: A 240 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7516 (pmm) REVERT: A 276 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: R 215 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8067 (t0) outliers start: 17 outliers final: 13 residues processed: 140 average time/residue: 0.2334 time to fit residues: 43.9480 Evaluate side-chains 144 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.0030 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8917 Z= 0.152 Angle : 0.505 14.875 12102 Z= 0.256 Chirality : 0.041 0.139 1414 Planarity : 0.003 0.047 1520 Dihedral : 4.599 57.593 1248 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.84 % Allowed : 13.99 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1126 helix: 1.30 (0.29), residues: 374 sheet: -0.00 (0.30), residues: 298 loop : -1.09 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 104 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE A 189 TYR 0.009 0.001 TYR B 59 ARG 0.006 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.072 Fit side-chains REVERT: A 229 ASP cc_start: 0.8046 (t70) cc_final: 0.7381 (t70) REVERT: A 240 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7488 (pmm) REVERT: A 276 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: R 104 TRP cc_start: 0.8475 (t-100) cc_final: 0.8198 (t60) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 0.2443 time to fit residues: 46.9676 Evaluate side-chains 143 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 340 ASN R 215 ASN R 257 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8917 Z= 0.223 Angle : 0.532 13.125 12102 Z= 0.273 Chirality : 0.042 0.142 1414 Planarity : 0.003 0.048 1520 Dihedral : 4.628 57.736 1248 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.28 % Allowed : 14.64 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.07 (0.26), residues: 1126 helix: 1.25 (0.29), residues: 374 sheet: -0.02 (0.30), residues: 298 loop : -1.13 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.005 0.001 HIS B 91 PHE 0.020 0.001 PHE S 68 TYR 0.011 0.001 TYR B 59 ARG 0.006 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.004 Fit side-chains REVERT: A 229 ASP cc_start: 0.8039 (t70) cc_final: 0.7354 (t70) REVERT: A 240 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7465 (pmm) REVERT: A 276 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: R 104 TRP cc_start: 0.8535 (t-100) cc_final: 0.8211 (t60) outliers start: 20 outliers final: 18 residues processed: 140 average time/residue: 0.2437 time to fit residues: 45.5633 Evaluate side-chains 148 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.0050 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8917 Z= 0.161 Angle : 0.496 8.977 12102 Z= 0.257 Chirality : 0.041 0.143 1414 Planarity : 0.003 0.048 1520 Dihedral : 4.544 56.985 1248 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.49 % Allowed : 14.53 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1126 helix: 1.32 (0.29), residues: 374 sheet: 0.05 (0.30), residues: 298 loop : -1.09 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.003 0.001 HIS B 91 PHE 0.018 0.001 PHE S 68 TYR 0.010 0.001 TYR B 59 ARG 0.006 0.000 ARG R 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.073 Fit side-chains REVERT: A 229 ASP cc_start: 0.8053 (t70) cc_final: 0.7367 (t70) REVERT: A 240 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7514 (pmm) REVERT: A 276 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: R 104 TRP cc_start: 0.8506 (t-100) cc_final: 0.8264 (t60) outliers start: 22 outliers final: 18 residues processed: 143 average time/residue: 0.2461 time to fit residues: 46.9196 Evaluate side-chains 149 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8917 Z= 0.137 Angle : 0.498 13.938 12102 Z= 0.252 Chirality : 0.040 0.138 1414 Planarity : 0.003 0.048 1520 Dihedral : 4.397 56.535 1248 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.49 % Allowed : 14.75 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.11 (0.26), residues: 1126 helix: 1.39 (0.29), residues: 374 sheet: 0.11 (0.30), residues: 298 loop : -1.04 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.003 0.000 HIS S 35 PHE 0.014 0.001 PHE S 68 TYR 0.008 0.001 TYR A 302 ARG 0.006 0.000 ARG R 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 0.978 Fit side-chains REVERT: A 229 ASP cc_start: 0.8066 (t70) cc_final: 0.7393 (t70) REVERT: A 240 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7503 (pmm) REVERT: A 273 LEU cc_start: 0.8736 (tt) cc_final: 0.8434 (tp) REVERT: A 276 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 330 LYS cc_start: 0.8083 (mptt) cc_final: 0.7653 (mptt) outliers start: 22 outliers final: 19 residues processed: 142 average time/residue: 0.2466 time to fit residues: 46.3482 Evaluate side-chains 147 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.0030 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.163294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114818 restraints weight = 26596.989| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 4.38 r_work: 0.3084 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8917 Z= 0.134 Angle : 0.491 11.927 12102 Z= 0.251 Chirality : 0.040 0.138 1414 Planarity : 0.003 0.048 1520 Dihedral : 4.298 56.310 1248 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.17 % Allowed : 15.51 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.18 (0.26), residues: 1126 helix: 1.49 (0.29), residues: 374 sheet: 0.13 (0.30), residues: 298 loop : -1.03 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 104 HIS 0.003 0.000 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.010 0.001 TYR R 165 ARG 0.006 0.000 ARG R 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.43 seconds wall clock time: 43 minutes 5.03 seconds (2585.03 seconds total)