Starting phenix.real_space_refine on Sat Feb 17 07:30:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2b_14460/02_2024/7z2b_14460_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2b_14460/02_2024/7z2b_14460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2b_14460/02_2024/7z2b_14460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2b_14460/02_2024/7z2b_14460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2b_14460/02_2024/7z2b_14460_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2b_14460/02_2024/7z2b_14460_trim_updated.pdb" } resolution = 3.3 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= 0.001 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: 7 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 5723 2.51 5 N 1575 2.21 5 O 1754 1.98 5 H 8797 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 320": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "H GLU 417": "OE1" <-> "OE2" 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: 17921 Number of models: 1 Model: "" Number of chains: 6 Chain: "K" Number of atoms: 4772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4772 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 7, 'TRANS': 300} Chain breaks: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 6569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6569 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 6482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6482 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.84, per 1000 atoms: 0.44 Number of scatterers: 17921 At special positions: 0 Unit cell: (98.7, 95.55, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 60 16.00 P 9 15.00 Mg 3 11.99 O 1754 8.00 N 1575 7.00 C 5723 6.00 H 8797 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 10 sheets defined 46.3% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'K' and resid 17 through 22 Processing helix chain 'K' and resid 71 through 78 Processing helix chain 'K' and resid 80 through 87 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 117 through 134 removed outlier: 3.999A pdb=" N ALA K 134 " --> pdb=" O LYS K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 160 No H-bonds generated for 'chain 'K' and resid 158 through 160' Processing helix chain 'K' and resid 186 through 198 Processing helix chain 'K' and resid 259 through 286 Processing helix chain 'K' and resid 296 through 298 No H-bonds generated for 'chain 'K' and resid 296 through 298' Processing helix chain 'K' and resid 300 through 309 removed outlier: 4.431A pdb=" N ASP K 307 " --> pdb=" O ARG K 303 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER K 308 " --> pdb=" O LEU K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 341 removed outlier: 5.182A pdb=" N GLU K 329 " --> pdb=" O LEU K 326 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR K 334 " --> pdb=" O THR K 331 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU K 335 " --> pdb=" O HIS K 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.609A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.557A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.079A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.587A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.408A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.601A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.539A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 415 through 435 Processing helix chain 'H' and resid 11 through 27 Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.555A pdb=" N GLU H 47 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 73 through 80 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.275A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 removed outlier: 3.666A pdb=" N GLY H 150 " --> pdb=" O GLY H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.544A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 224 through 243 removed outlier: 3.813A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 340 through 342 No H-bonds generated for 'chain 'H' and resid 340 through 342' Processing helix chain 'H' and resid 382 through 401 removed outlier: 3.770A pdb=" N ARG H 390 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG H 400 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 Processing helix chain 'H' and resid 415 through 435 Processing sheet with id= A, first strand: chain 'K' and resid 63 through 65 removed outlier: 3.859A pdb=" N TYR K 63 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ASN K 7 " --> pdb=" O CYS K 313 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR K 315 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL K 9 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET K 317 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG K 11 " --> pdb=" O MET K 317 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA K 319 " --> pdb=" O ARG K 11 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG K 13 " --> pdb=" O ALA K 319 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE K 321 " --> pdb=" O ARG K 13 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN K 91 " --> pdb=" O LYS K 314 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LEU K 316 " --> pdb=" O ASN K 91 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR K 93 " --> pdb=" O LEU K 316 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE K 318 " --> pdb=" O THR K 93 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE K 95 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN K 320 " --> pdb=" O PHE K 95 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR K 97 " --> pdb=" O ASN K 320 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N SER K 322 " --> pdb=" O TYR K 97 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER K 92 " --> pdb=" O LYS K 237 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS K 239 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL K 94 " --> pdb=" O LYS K 239 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS K 241 " --> pdb=" O VAL K 94 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA K 96 " --> pdb=" O CYS K 241 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE K 243 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 57 through 60 removed outlier: 6.411A pdb=" N VAL K 37 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE K 30 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 145 through 148 Processing sheet with id= D, first strand: chain 'K' and resid 165 through 167 Processing sheet with id= E, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.020A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 131 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE A 5 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLN A 133 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N ILE A 7 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE A 135 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N VAL A 9 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N VAL A 137 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.632A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL H 172 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE H 204 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.891A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 269 through 273 405 hydrogen bonds defined for protein. 1053 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: 6.29 Time building geometry restraints manager: 14.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8771 1.03 - 1.23: 482 1.23 - 1.43: 3449 1.43 - 1.62: 5302 1.62 - 1.82: 98 Bond restraints: 18102 Sorted by residual: bond pdb=" N3B ANP K 401 " pdb=" PG ANP K 401 " ideal model delta sigma weight residual 1.795 1.611 0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" O3A ANP K 401 " pdb=" PB ANP K 401 " ideal model delta sigma weight residual 1.700 1.574 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C GLY A 412 " pdb=" O GLY A 412 " ideal model delta sigma weight residual 1.235 1.308 -0.073 1.35e-02 5.49e+03 2.91e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" O2A G2P H 501 " pdb=" PA G2P H 501 " ideal model delta sigma weight residual 1.513 1.610 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 18097 not shown) Histogram of bond angle deviations from ideal: 77.63 - 89.61: 3 89.61 - 101.59: 49 101.59 - 113.57: 21160 113.57 - 125.55: 11073 125.55 - 137.53: 319 Bond angle restraints: 32604 Sorted by residual: angle pdb=" C3' ANP K 401 " pdb=" C4' ANP K 401 " pdb=" C5' ANP K 401 " ideal model delta sigma weight residual 116.03 88.17 27.86 3.00e+00 1.11e-01 8.63e+01 angle pdb=" O2A ANP K 401 " pdb=" PA ANP K 401 " pdb=" O5' ANP K 401 " ideal model delta sigma weight residual 108.82 85.68 23.14 3.00e+00 1.11e-01 5.95e+01 angle pdb=" O3A ANP K 401 " pdb=" PA ANP K 401 " pdb=" O5' ANP K 401 " ideal model delta sigma weight residual 98.09 77.63 20.46 3.00e+00 1.11e-01 4.65e+01 angle pdb=" C SER K 322 " pdb=" N PRO K 323 " pdb=" CA PRO K 323 " ideal model delta sigma weight residual 119.56 126.24 -6.68 1.01e+00 9.80e-01 4.37e+01 angle pdb=" N ILE K 173 " pdb=" CA ILE K 173 " pdb=" C ILE K 173 " ideal model delta sigma weight residual 108.12 117.58 -9.46 1.44e+00 4.82e-01 4.32e+01 ... (remaining 32599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 8260 34.65 - 69.30: 314 69.30 - 103.95: 17 103.95 - 138.61: 0 138.61 - 173.26: 4 Dihedral angle restraints: 8595 sinusoidal: 4670 harmonic: 3925 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.68 -168.05 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -51.76 156.35 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 134.43 139.70 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 8592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1133 0.114 - 0.228: 242 0.228 - 0.343: 26 0.343 - 0.457: 2 0.457 - 0.571: 1 Chirality restraints: 1404 Sorted by residual: chirality pdb=" C4' ANP K 401 " pdb=" C3' ANP K 401 " pdb=" C5' ANP K 401 " pdb=" O4' ANP K 401 " both_signs ideal model delta sigma weight residual False -2.45 -3.02 0.57 2.00e-01 2.50e+01 8.15e+00 chirality pdb=" CA HIS A 197 " pdb=" N HIS A 197 " pdb=" C HIS A 197 " pdb=" CB HIS A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PHE K 126 " pdb=" N PHE K 126 " pdb=" C PHE K 126 " pdb=" CB PHE K 126 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 1401 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 333 " 0.100 2.00e-02 2.50e+03 1.06e-01 1.68e+02 pdb=" CG ASN K 333 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN K 333 " -0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN K 333 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN K 333 " 0.160 2.00e-02 2.50e+03 pdb="HD22 ASN K 333 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 266 " -0.084 2.00e-02 2.50e+03 9.00e-02 1.21e+02 pdb=" CG ASN K 266 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN K 266 " 0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN K 266 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN K 266 " -0.136 2.00e-02 2.50e+03 pdb="HD22 ASN K 266 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 75 " 0.055 2.00e-02 2.50e+03 2.68e-02 2.16e+01 pdb=" CG TYR K 75 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR K 75 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR K 75 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR K 75 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR K 75 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR K 75 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR K 75 " 0.051 2.00e-02 2.50e+03 pdb=" HD1 TYR K 75 " -0.039 2.00e-02 2.50e+03 pdb=" HD2 TYR K 75 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TYR K 75 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR K 75 " -0.030 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.78: 16 1.78 - 2.48: 11899 2.48 - 3.19: 55994 3.19 - 3.89: 72179 3.89 - 4.60: 115637 Nonbonded interactions: 255725 Sorted by model distance: nonbonded pdb=" NZ LYS K 171 " pdb=" OG SER H 423 " model vdw 1.073 2.350 nonbonded pdb=" NZ LYS K 336 " pdb=" OG SER A 419 " model vdw 1.165 2.350 nonbonded pdb=" CZ ARG K 340 " pdb=" NH2 ARG A 402 " model vdw 1.230 3.250 nonbonded pdb=" NH2 ARG K 340 " pdb=" NH2 ARG A 402 " model vdw 1.240 3.100 nonbonded pdb=" NH1 ARG K 340 " pdb=" NH2 ARG A 402 " model vdw 1.323 3.100 ... (remaining 255720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.590 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: 0.250 Extract box with map and model: 37.570 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 57.590 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 : 0.012 0.184 9305 Z= 0.811 Angle : 1.720 27.864 12618 Z= 1.132 Chirality : 0.092 0.571 1404 Planarity : 0.008 0.074 1625 Dihedral : 15.625 173.258 3450 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.14 % Favored : 96.68 % Rotamer: Outliers : 0.62 % Allowed : 6.06 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1146 helix: 0.50 (0.21), residues: 499 sheet: -0.24 (0.36), residues: 214 loop : -0.85 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 21 HIS 0.014 0.002 HIS A 88 PHE 0.037 0.003 PHE K 61 TYR 0.045 0.005 TYR K 97 ARG 0.007 0.001 ARG K 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 222 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.6056 (pttt) outliers start: 6 outliers final: 1 residues processed: 227 average time/residue: 0.6176 time to fit residues: 180.5738 Evaluate side-chains 143 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain A residue 326 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.0870 chunk 66 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 26 ASN K 197 ASN K 325 HIS A 61 HIS A 192 HIS A 197 HIS ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9305 Z= 0.251 Angle : 0.676 7.406 12618 Z= 0.366 Chirality : 0.043 0.143 1404 Planarity : 0.005 0.082 1625 Dihedral : 12.698 173.370 1339 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 1.34 % Allowed : 12.44 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1146 helix: 1.28 (0.22), residues: 504 sheet: -0.23 (0.35), residues: 205 loop : -0.68 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 21 HIS 0.007 0.001 HIS A 192 PHE 0.021 0.002 PHE K 144 TYR 0.014 0.002 TYR K 75 ARG 0.009 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 147 average time/residue: 0.5191 time to fit residues: 103.8559 Evaluate side-chains 129 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 191 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 chunk 92 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 83 optimal weight: 0.0070 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 192 HIS ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9305 Z= 0.198 Angle : 0.567 5.849 12618 Z= 0.304 Chirality : 0.041 0.138 1404 Planarity : 0.004 0.051 1625 Dihedral : 11.612 174.144 1335 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 1.54 % Allowed : 13.16 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.63 (0.25), residues: 1146 helix: 1.55 (0.23), residues: 508 sheet: -0.24 (0.35), residues: 206 loop : -0.52 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 21 HIS 0.010 0.001 HIS A 192 PHE 0.024 0.002 PHE A 255 TYR 0.017 0.001 TYR K 75 ARG 0.004 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.4766 time to fit residues: 90.7116 Evaluate side-chains 122 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 248 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9305 Z= 0.347 Angle : 0.600 6.053 12618 Z= 0.326 Chirality : 0.041 0.144 1404 Planarity : 0.004 0.039 1625 Dihedral : 11.321 174.837 1333 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 2.16 % Allowed : 13.16 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1146 helix: 1.18 (0.23), residues: 511 sheet: -0.43 (0.35), residues: 207 loop : -0.43 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 21 HIS 0.005 0.001 HIS A 28 PHE 0.018 0.002 PHE A 255 TYR 0.015 0.002 TYR K 75 ARG 0.005 0.001 ARG H 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 35 MET cc_start: 0.4329 (tpt) cc_final: 0.3287 (tpt) outliers start: 21 outliers final: 20 residues processed: 124 average time/residue: 0.4830 time to fit residues: 83.4645 Evaluate side-chains 128 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 266 ASN Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 194 HIS K 279 ASN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN A 133 GLN A 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9305 Z= 0.365 Angle : 0.611 9.598 12618 Z= 0.327 Chirality : 0.042 0.141 1404 Planarity : 0.004 0.065 1625 Dihedral : 11.146 170.527 1333 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 2.36 % Allowed : 13.57 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.25), residues: 1146 helix: 0.78 (0.23), residues: 513 sheet: -0.29 (0.38), residues: 189 loop : -0.54 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 21 HIS 0.006 0.001 HIS H 266 PHE 0.019 0.002 PHE A 255 TYR 0.016 0.002 TYR A 172 ARG 0.022 0.001 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 119 MET cc_start: 0.3739 (tpp) cc_final: 0.2055 (tpp) outliers start: 23 outliers final: 20 residues processed: 121 average time/residue: 0.4693 time to fit residues: 80.9353 Evaluate side-chains 120 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 0.0070 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9305 Z= 0.276 Angle : 0.561 6.843 12618 Z= 0.298 Chirality : 0.040 0.134 1404 Planarity : 0.004 0.051 1625 Dihedral : 11.055 169.720 1333 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.67 % Allowed : 13.77 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1146 helix: 0.85 (0.23), residues: 513 sheet: -0.15 (0.38), residues: 186 loop : -0.55 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.019 0.002 PHE A 255 TYR 0.010 0.001 TYR A 172 ARG 0.004 0.000 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 22 residues processed: 124 average time/residue: 0.4192 time to fit residues: 75.4553 Evaluate side-chains 122 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 142 CYS Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 266 ASN Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 405 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9305 Z= 0.338 Angle : 0.590 6.653 12618 Z= 0.313 Chirality : 0.041 0.144 1404 Planarity : 0.004 0.040 1625 Dihedral : 11.066 168.016 1333 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 2.88 % Allowed : 13.26 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.25), residues: 1146 helix: 0.61 (0.23), residues: 513 sheet: -0.30 (0.38), residues: 194 loop : -0.65 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.022 0.002 PHE A 255 TYR 0.012 0.001 TYR K 148 ARG 0.003 0.000 ARG H 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6955 (t80) outliers start: 28 outliers final: 24 residues processed: 115 average time/residue: 0.3988 time to fit residues: 68.3216 Evaluate side-chains 124 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 142 CYS Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 405 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9305 Z= 0.277 Angle : 0.558 6.158 12618 Z= 0.295 Chirality : 0.040 0.135 1404 Planarity : 0.004 0.040 1625 Dihedral : 10.916 168.207 1333 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 2.36 % Allowed : 14.49 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 1146 helix: 0.81 (0.23), residues: 511 sheet: -0.13 (0.39), residues: 187 loop : -0.58 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.007 0.001 HIS K 215 PHE 0.023 0.002 PHE A 255 TYR 0.009 0.001 TYR H 435 ARG 0.003 0.000 ARG H 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7026 (t80) outliers start: 23 outliers final: 22 residues processed: 116 average time/residue: 0.3957 time to fit residues: 68.4645 Evaluate side-chains 122 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 142 CYS Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 405 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9305 Z= 0.318 Angle : 0.582 6.787 12618 Z= 0.307 Chirality : 0.041 0.141 1404 Planarity : 0.004 0.039 1625 Dihedral : 10.943 167.058 1333 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 2.77 % Allowed : 14.59 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.03 (0.25), residues: 1146 helix: 0.66 (0.23), residues: 512 sheet: -0.16 (0.40), residues: 186 loop : -0.62 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 21 HIS 0.006 0.001 HIS A 88 PHE 0.022 0.002 PHE A 255 TYR 0.011 0.001 TYR H 435 ARG 0.003 0.000 ARG H 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6967 (t80) outliers start: 27 outliers final: 24 residues processed: 115 average time/residue: 0.3978 time to fit residues: 67.3207 Evaluate side-chains 123 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 142 CYS Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 405 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.2980 chunk 75 optimal weight: 0.1980 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 overall best weight: 0.1496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9305 Z= 0.152 Angle : 0.536 7.654 12618 Z= 0.273 Chirality : 0.040 0.139 1404 Planarity : 0.003 0.038 1625 Dihedral : 10.560 164.367 1333 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 1.95 % Allowed : 15.42 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.55 (0.26), residues: 1146 helix: 1.24 (0.24), residues: 510 sheet: 0.06 (0.40), residues: 184 loop : -0.41 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.023 0.001 PHE A 255 TYR 0.013 0.001 TYR A 24 ARG 0.002 0.000 ARG H 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6973 (t80) outliers start: 19 outliers final: 17 residues processed: 119 average time/residue: 0.4145 time to fit residues: 73.1828 Evaluate side-chains 116 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 405 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.0030 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.066495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.048635 restraints weight = 90706.644| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.90 r_work: 0.2949 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9305 Z= 0.267 Angle : 0.564 8.020 12618 Z= 0.293 Chirality : 0.040 0.139 1404 Planarity : 0.003 0.038 1625 Dihedral : 10.622 162.944 1333 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 1.95 % Allowed : 16.14 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.26), residues: 1146 helix: 1.08 (0.24), residues: 511 sheet: 0.03 (0.40), residues: 184 loop : -0.51 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.021 0.002 PHE A 255 TYR 0.011 0.001 TYR K 148 ARG 0.002 0.000 ARG K 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5261.24 seconds wall clock time: 95 minutes 11.97 seconds (5711.97 seconds total)