Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 00:53:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/04_2023/8id3_35356_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/04_2023/8id3_35356.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/04_2023/8id3_35356_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/04_2023/8id3_35356_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/04_2023/8id3_35356_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/04_2023/8id3_35356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/04_2023/8id3_35356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/04_2023/8id3_35356_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id3_35356/04_2023/8id3_35356_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.70, per 1000 atoms: 0.65 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: 3.83 Conformation dependent library (CDL) restraints added in 1.7 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: 0.80 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: 2.35 Time building geometry restraints manager: 4.09 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 - 27.14: 5060 27.14 - 54.29: 177 54.29 - 81.43: 25 81.43 - 108.58: 4 108.58 - 135.72: 2 Dihedral angle restraints: 5268 sinusoidal: 1958 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=" C13 7NR R 401 " pdb=" C15 7NR R 401 " pdb=" C17 7NR R 401 " pdb=" C19 7NR R 401 " ideal model delta sinusoidal sigma weight residual 192.01 56.29 135.72 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 5265 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: 1 0.263 - 0.329: 1 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 -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.50e+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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.290 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.180 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.070 ------------------------------------------------------------------------------- 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= 0.296 Angle : 0.869 26.993 12102 Z= 0.508 Chirality : 0.047 0.329 1414 Planarity : 0.015 0.476 1520 Dihedral : 14.378 135.722 3123 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 % 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 *********************** 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 : 1.084 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 161 average time/residue: 0.2396 time to fit residues: 51.9796 Evaluate side-chains 138 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0833 time to fit residues: 1.5517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7536 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 8917 Z= 0.154 Angle : 0.518 7.027 12102 Z= 0.270 Chirality : 0.041 0.137 1414 Planarity : 0.004 0.048 1520 Dihedral : 7.758 109.184 1241 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.30 % 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: 0.67 (0.28), residues: 365 sheet: -0.41 (0.30), residues: 288 loop : -1.31 (0.28), residues: 473 *********************** 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 163 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 1.029 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 153 average time/residue: 0.2490 time to fit residues: 50.4898 Evaluate side-chains 146 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0847 time to fit residues: 2.5047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 8917 Z= 0.150 Angle : 0.503 7.271 12102 Z= 0.260 Chirality : 0.041 0.134 1414 Planarity : 0.003 0.045 1520 Dihedral : 7.040 99.070 1241 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.08 % 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: -0.34 (0.25), residues: 1126 helix: 1.07 (0.29), residues: 363 sheet: -0.22 (0.30), residues: 290 loop : -1.21 (0.28), residues: 473 *********************** 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 151 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 1.064 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 147 average time/residue: 0.2535 time to fit residues: 50.1509 Evaluate side-chains 140 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0847 time to fit residues: 2.2428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN A 195 HIS R 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1508 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 : 0.498 7.409 12102 Z= 0.259 Chirality : 0.041 0.134 1414 Planarity : 0.003 0.045 1520 Dihedral : 6.652 102.231 1241 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.19 % 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 (0.25), residues: 1126 helix: 1.26 (0.29), residues: 365 sheet: -0.08 (0.30), residues: 292 loop : -1.10 (0.28), residues: 469 *********************** 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 147 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.086 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 140 average time/residue: 0.2432 time to fit residues: 45.9681 Evaluate side-chains 136 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0898 time to fit residues: 2.5867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 215 ASN R 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8917 Z= 0.220 Angle : 0.523 7.169 12102 Z= 0.274 Chirality : 0.042 0.136 1414 Planarity : 0.003 0.045 1520 Dihedral : 6.514 100.043 1241 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 1.08 % 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: -0.16 (0.25), residues: 1126 helix: 1.16 (0.29), residues: 372 sheet: -0.06 (0.30), residues: 297 loop : -1.16 (0.28), residues: 457 *********************** 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 143 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.116 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 137 average time/residue: 0.2554 time to fit residues: 46.7200 Evaluate side-chains 134 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0838 time to fit residues: 2.1670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1784 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= 0.128 Angle : 0.480 9.745 12102 Z= 0.248 Chirality : 0.040 0.137 1414 Planarity : 0.003 0.045 1520 Dihedral : 5.997 89.821 1241 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.19 % 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: -0.01 (0.26), residues: 1126 helix: 1.30 (0.29), residues: 378 sheet: 0.03 (0.30), residues: 292 loop : -1.11 (0.28), residues: 456 *********************** 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 139 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.988 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 135 average time/residue: 0.2361 time to fit residues: 42.9520 Evaluate side-chains 135 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0852 time to fit residues: 2.3328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 8917 Z= 0.154 Angle : 0.488 11.250 12102 Z= 0.252 Chirality : 0.040 0.135 1414 Planarity : 0.003 0.046 1520 Dihedral : 5.585 70.967 1241 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.19 % 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: 1.37 (0.29), residues: 375 sheet: 0.09 (0.30), residues: 293 loop : -1.07 (0.28), residues: 458 *********************** 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 140 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.999 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 134 average time/residue: 0.2459 time to fit residues: 44.1094 Evaluate side-chains 133 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0871 time to fit residues: 2.3483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1940 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= 0.138 Angle : 0.486 12.766 12102 Z= 0.249 Chirality : 0.040 0.139 1414 Planarity : 0.003 0.046 1520 Dihedral : 5.295 63.373 1241 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.54 % 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: 0.13 (0.26), residues: 1126 helix: 1.37 (0.29), residues: 381 sheet: 0.18 (0.30), residues: 288 loop : -1.06 (0.28), residues: 457 *********************** 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 133 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.031 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 132 average time/residue: 0.2524 time to fit residues: 44.7886 Evaluate side-chains 128 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0838 time to fit residues: 1.7073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.0000 chunk 94 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 0.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2093 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= 0.126 Angle : 0.481 12.330 12102 Z= 0.245 Chirality : 0.040 0.137 1414 Planarity : 0.003 0.046 1520 Dihedral : 4.990 63.373 1241 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.43 % 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: 0.25 (0.26), residues: 1126 helix: 1.53 (0.29), residues: 376 sheet: 0.21 (0.30), residues: 290 loop : -0.99 (0.29), residues: 460 *********************** 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 142 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 0.943 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 140 average time/residue: 0.2422 time to fit residues: 45.5040 Evaluate side-chains 127 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0835 time to fit residues: 1.5411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2046 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= 0.183 Angle : 0.510 12.584 12102 Z= 0.262 Chirality : 0.041 0.134 1414 Planarity : 0.003 0.046 1520 Dihedral : 5.051 64.355 1241 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.22 % 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: 0.24 (0.26), residues: 1126 helix: 1.47 (0.29), residues: 379 sheet: 0.21 (0.30), residues: 293 loop : -0.98 (0.29), residues: 454 ********************** 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 128 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.047 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.2512 time to fit residues: 42.8477 Evaluate side-chains 125 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1018 time to fit residues: 1.9118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 90 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 overall best weight: 0.9458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113212 restraints weight = 26709.677| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.18 r_work: 0.3121 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2074 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= 0.167 Angle : 0.504 13.222 12102 Z= 0.258 Chirality : 0.041 0.135 1414 Planarity : 0.003 0.046 1520 Dihedral : 4.947 63.929 1241 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.33 % 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: 0.26 (0.26), residues: 1126 helix: 1.49 (0.29), residues: 379 sheet: 0.22 (0.30), residues: 293 loop : -0.95 (0.29), residues: 454 =============================================================================== Job complete usr+sys time: 2116.59 seconds wall clock time: 38 minutes 58.73 seconds (2338.73 seconds total)