Starting phenix.real_space_refine on Fri Mar 15 08:51:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/03_2024/6x19_21993_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/03_2024/6x19_21993.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/03_2024/6x19_21993_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/03_2024/6x19_21993_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/03_2024/6x19_21993_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/03_2024/6x19_21993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/03_2024/6x19_21993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/03_2024/6x19_21993_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/03_2024/6x19_21993_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 843 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 62 5.16 5 C 6462 2.51 5 N 1748 2.21 5 O 2003 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R GLU 76": "OE1" <-> "OE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10277 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2876 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3268 Unusual residues: {'UK1': 1} Classifications: {'peptide': 387, 'undetermined': 1} Link IDs: {'PTRANS': 14, 'TRANS': 372, None: 1} Not linked: pdbres="GLU R 423 " pdbres="UK1 R 501 " Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 5.62, per 1000 atoms: 0.55 Number of scatterers: 10277 At special positions: 0 Unit cell: (115.37, 96.28, 170.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 F 2 9.00 O 2003 8.00 N 1748 7.00 C 6462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.01 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.05 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 11 sheets defined 41.3% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.990A pdb=" N GLN A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 109 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.848A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.728A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.548A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'R' and resid 32 through 52 removed outlier: 4.029A pdb=" N GLN R 37 " --> pdb=" O TRP R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 116 No H-bonds generated for 'chain 'R' and resid 114 through 116' Processing helix chain 'R' and resid 124 through 126 No H-bonds generated for 'chain 'R' and resid 124 through 126' Processing helix chain 'R' and resid 137 through 140 No H-bonds generated for 'chain 'R' and resid 137 through 140' Processing helix chain 'R' and resid 142 through 166 Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing helix chain 'R' and resid 175 through 207 Processing helix chain 'R' and resid 211 through 222 removed outlier: 5.074A pdb=" N ASP R 215 " --> pdb=" O HIS R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 256 Processing helix chain 'R' and resid 262 through 274 removed outlier: 3.698A pdb=" N PHE R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 291 removed outlier: 3.686A pdb=" N VAL R 281 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL R 282 " --> pdb=" O LEU R 279 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.504A pdb=" N VAL R 287 " --> pdb=" O TRP R 284 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR R 291 " --> pdb=" O LYS R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 337 removed outlier: 5.282A pdb=" N LEU R 311 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.602A pdb=" N PHE R 315 " --> pdb=" O PRO R 312 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL R 319 " --> pdb=" O ALA R 316 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 322 " --> pdb=" O VAL R 319 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL R 327 " --> pdb=" O PHE R 324 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS R 329 " --> pdb=" O ARG R 326 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS R 336 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 369 Processing helix chain 'R' and resid 379 through 392 removed outlier: 3.691A pdb=" N LYS R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 402 Processing helix chain 'R' and resid 407 through 422 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.099A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.892A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.764A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.555A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.738A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.605A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.439A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.562A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 93 through 98 removed outlier: 5.970A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 80 through 83 451 hydrogen bonds defined for protein. 1149 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: 2.91 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1661 1.32 - 1.44: 2925 1.44 - 1.57: 5697 1.57 - 1.69: 11 1.69 - 1.82: 85 Bond restraints: 10379 Sorted by residual: bond pdb=" C03 UK1 R 501 " pdb=" N07 UK1 R 501 " ideal model delta sigma weight residual 1.478 1.722 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C46 UK1 R 501 " pdb=" C51 UK1 R 501 " ideal model delta sigma weight residual 1.390 1.546 -0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C28 UK1 R 501 " pdb=" C60 UK1 R 501 " ideal model delta sigma weight residual 1.524 1.674 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C46 UK1 R 501 " pdb=" N43 UK1 R 501 " ideal model delta sigma weight residual 1.481 1.628 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C25 UK1 R 501 " pdb=" N24 UK1 R 501 " ideal model delta sigma weight residual 1.384 1.516 -0.132 2.00e-02 2.50e+03 4.39e+01 ... (remaining 10374 not shown) Histogram of bond angle deviations from ideal: 70.00 - 83.47: 1 83.47 - 96.94: 0 96.94 - 110.41: 2475 110.41 - 123.87: 11019 123.87 - 137.34: 591 Bond angle restraints: 14086 Sorted by residual: angle pdb=" C21 UK1 R 501 " pdb=" C23 UK1 R 501 " pdb=" C27 UK1 R 501 " ideal model delta sigma weight residual 62.25 125.89 -63.64 3.00e+00 1.11e-01 4.50e+02 angle pdb=" C28 UK1 R 501 " pdb=" C57 UK1 R 501 " pdb=" C58 UK1 R 501 " ideal model delta sigma weight residual 109.49 70.00 39.49 3.00e+00 1.11e-01 1.73e+02 angle pdb=" N PRO A 115 " pdb=" CA PRO A 115 " pdb=" C PRO A 115 " ideal model delta sigma weight residual 110.70 99.23 11.47 1.22e+00 6.72e-01 8.83e+01 angle pdb=" C PHE A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta sigma weight residual 119.66 125.30 -5.64 7.30e-01 1.88e+00 5.96e+01 angle pdb=" N ASN A 14 " pdb=" CA ASN A 14 " pdb=" C ASN A 14 " ideal model delta sigma weight residual 113.41 105.34 8.07 1.22e+00 6.72e-01 4.37e+01 ... (remaining 14081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.04: 5688 20.04 - 40.07: 389 40.07 - 60.11: 47 60.11 - 80.15: 21 80.15 - 100.18: 6 Dihedral angle restraints: 6151 sinusoidal: 2466 harmonic: 3685 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C ASN A 371 " pdb=" N ASN A 371 " pdb=" CA ASN A 371 " pdb=" CB ASN A 371 " ideal model delta harmonic sigma weight residual -122.60 -135.35 12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ARG A 317 " pdb=" N ARG A 317 " pdb=" CA ARG A 317 " pdb=" CB ARG A 317 " ideal model delta harmonic sigma weight residual -122.60 -110.51 -12.09 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 6148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1275 0.090 - 0.179: 200 0.179 - 0.269: 45 0.269 - 0.358: 17 0.358 - 0.448: 5 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ASP R 293 " pdb=" N ASP R 293 " pdb=" C ASP R 293 " pdb=" CB ASP R 293 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C28 UK1 R 501 " pdb=" C57 UK1 R 501 " pdb=" C60 UK1 R 501 " pdb=" N24 UK1 R 501 " both_signs ideal model delta sigma weight residual False -2.64 -2.20 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA ASN A 371 " pdb=" N ASN A 371 " pdb=" C ASN A 371 " pdb=" CB ASN A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 1539 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 290 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C LEU R 290 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU R 290 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR R 291 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 101 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C TYR R 101 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR R 101 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG R 102 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 155 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C GLU A 155 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU A 155 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 156 " -0.015 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 303 2.69 - 3.24: 10570 3.24 - 3.79: 16952 3.79 - 4.35: 24311 4.35 - 4.90: 37159 Nonbonded interactions: 89295 Sorted by model distance: nonbonded pdb=" OH TYR B 105 " pdb=" O HOH B 401 " model vdw 2.134 2.440 nonbonded pdb=" OD1 ASP A 141 " pdb=" CD PRO A 143 " model vdw 2.158 3.440 nonbonded pdb=" OE1 GLU A 392 " pdb=" O HOH A 401 " model vdw 2.185 2.440 nonbonded pdb=" OE2 GLU A 209 " pdb=" O HOH A 402 " model vdw 2.244 2.440 nonbonded pdb=" N GLU A 145 " pdb=" OE1 GLU A 145 " model vdw 2.269 2.520 ... (remaining 89290 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=0.00 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 5.660 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 31.040 Find NCS groups from input model: 0.330 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.009 0.244 10379 Z= 0.630 Angle : 1.295 63.641 14086 Z= 0.793 Chirality : 0.079 0.448 1542 Planarity : 0.005 0.047 1793 Dihedral : 14.322 100.185 3747 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.26 % Rotamer: Outliers : 1.01 % Allowed : 4.04 % Favored : 94.95 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.22), residues: 1240 helix: -1.26 (0.20), residues: 519 sheet: -0.58 (0.31), residues: 241 loop : -0.83 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 87 HIS 0.011 0.001 HIS A 357 PHE 0.018 0.002 PHE A 363 TYR 0.030 0.002 TYR B 59 ARG 0.005 0.001 ARG R 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.8032 (pt0) cc_final: 0.7744 (pt0) REVERT: A 344 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7435 (mm-30) REVERT: R 117 SER cc_start: 0.2598 (OUTLIER) cc_final: 0.1520 (t) REVERT: R 267 ARG cc_start: 0.6435 (mmt180) cc_final: 0.6220 (tpt170) outliers start: 11 outliers final: 1 residues processed: 187 average time/residue: 1.5069 time to fit residues: 298.4119 Evaluate side-chains 125 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 117 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS B 44 GLN B 88 ASN B 176 GLN B 268 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 31 ASN R 45 GLN R 99 HIS R 140 GLN R 338 ASN R 407 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10379 Z= 0.194 Angle : 0.749 39.853 14086 Z= 0.355 Chirality : 0.043 0.229 1542 Planarity : 0.005 0.043 1793 Dihedral : 6.638 93.111 1396 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.38 % Allowed : 10.64 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.23), residues: 1240 helix: 0.23 (0.21), residues: 524 sheet: -0.22 (0.32), residues: 246 loop : -0.27 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 87 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE R 80 TYR 0.031 0.002 TYR R 148 ARG 0.008 0.000 ARG R 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.0944 (tmm) cc_final: 0.0617 (tmm) REVERT: B 59 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: B 188 MET cc_start: 0.8845 (mmm) cc_final: 0.8587 (mmm) outliers start: 15 outliers final: 4 residues processed: 132 average time/residue: 1.6418 time to fit residues: 229.5217 Evaluate side-chains 118 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 120 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 176 GLN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10379 Z= 0.207 Angle : 0.729 38.063 14086 Z= 0.339 Chirality : 0.042 0.153 1542 Planarity : 0.004 0.049 1793 Dihedral : 6.625 96.694 1394 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.57 % Allowed : 11.56 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.24), residues: 1240 helix: 0.83 (0.22), residues: 524 sheet: 0.01 (0.32), residues: 254 loop : -0.06 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.002 PHE B 151 TYR 0.029 0.002 TYR R 148 ARG 0.005 0.000 ARG R 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6377 (mmtp) REVERT: B 59 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: B 340 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7527 (t0) REVERT: N 19 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7643 (ttt180) REVERT: R 41 GLU cc_start: 0.7464 (tp30) cc_final: 0.7121 (tp30) REVERT: R 336 LYS cc_start: 0.7735 (mmtp) cc_final: 0.7534 (mttm) REVERT: R 344 ASP cc_start: 0.6065 (t0) cc_final: 0.5851 (t0) outliers start: 28 outliers final: 11 residues processed: 131 average time/residue: 1.6572 time to fit residues: 229.5907 Evaluate side-chains 123 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 12 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 268 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN R 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10379 Z= 0.389 Angle : 0.813 36.641 14086 Z= 0.388 Chirality : 0.048 0.194 1542 Planarity : 0.005 0.051 1793 Dihedral : 7.033 98.851 1394 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 12.75 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.23), residues: 1240 helix: 0.72 (0.22), residues: 523 sheet: 0.22 (0.33), residues: 233 loop : -0.18 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.025 0.002 PHE B 151 TYR 0.025 0.002 TYR R 148 ARG 0.005 0.001 ARG R 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6381 (mmtp) REVERT: B 59 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: G 20 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8295 (mtpt) REVERT: N 19 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7759 (ttt180) REVERT: R 336 LYS cc_start: 0.7812 (mmtp) cc_final: 0.7595 (mmtm) REVERT: R 344 ASP cc_start: 0.6148 (t0) cc_final: 0.5943 (t0) outliers start: 27 outliers final: 12 residues processed: 131 average time/residue: 1.6643 time to fit residues: 230.6754 Evaluate side-chains 128 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10379 Z= 0.204 Angle : 0.713 37.719 14086 Z= 0.328 Chirality : 0.042 0.158 1542 Planarity : 0.004 0.052 1793 Dihedral : 6.577 94.793 1394 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.48 % Allowed : 13.76 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.24), residues: 1240 helix: 1.04 (0.22), residues: 529 sheet: 0.26 (0.33), residues: 238 loop : 0.01 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.024 0.002 TYR R 148 ARG 0.013 0.000 ARG R 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6387 (mmtp) REVERT: B 59 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: B 340 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7541 (t0) REVERT: G 42 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: N 19 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7660 (ttt180) REVERT: R 336 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7577 (mmtm) outliers start: 27 outliers final: 10 residues processed: 131 average time/residue: 1.6489 time to fit residues: 228.7034 Evaluate side-chains 125 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 88 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10379 Z= 0.153 Angle : 0.675 37.611 14086 Z= 0.305 Chirality : 0.040 0.177 1542 Planarity : 0.004 0.053 1793 Dihedral : 6.285 94.792 1394 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.20 % Allowed : 14.22 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.24), residues: 1240 helix: 1.34 (0.23), residues: 528 sheet: 0.36 (0.34), residues: 228 loop : 0.07 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 280 TYR 0.024 0.001 TYR R 148 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.6386 (mmpt) cc_final: 0.6178 (mmpt) REVERT: B 15 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.8015 (mttm) REVERT: B 59 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: G 20 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8392 (mtpt) REVERT: G 42 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: N 19 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7613 (ttt180) REVERT: R 110 TRP cc_start: 0.4275 (m100) cc_final: 0.3955 (m100) REVERT: R 336 LYS cc_start: 0.7799 (mmtp) cc_final: 0.7573 (mmtm) outliers start: 24 outliers final: 9 residues processed: 126 average time/residue: 1.6203 time to fit residues: 216.1465 Evaluate side-chains 122 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 118 optimal weight: 0.2980 chunk 74 optimal weight: 0.0170 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10379 Z= 0.133 Angle : 0.665 37.654 14086 Z= 0.297 Chirality : 0.040 0.194 1542 Planarity : 0.004 0.052 1793 Dihedral : 6.094 94.063 1394 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.65 % Allowed : 14.86 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.24), residues: 1240 helix: 1.53 (0.23), residues: 526 sheet: 0.48 (0.34), residues: 225 loop : 0.17 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.023 0.001 TYR R 148 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: G 42 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: N 19 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7556 (ttt180) REVERT: R 110 TRP cc_start: 0.4381 (m100) cc_final: 0.4057 (m100) REVERT: R 301 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7521 (m) REVERT: R 336 LYS cc_start: 0.7759 (mmtp) cc_final: 0.7551 (mmtm) outliers start: 18 outliers final: 6 residues processed: 126 average time/residue: 1.5760 time to fit residues: 210.6624 Evaluate side-chains 118 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 301 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN B 16 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10379 Z= 0.176 Angle : 0.697 37.292 14086 Z= 0.314 Chirality : 0.041 0.156 1542 Planarity : 0.004 0.052 1793 Dihedral : 6.325 97.484 1394 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.19 % Allowed : 14.95 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1240 helix: 1.48 (0.23), residues: 526 sheet: 0.36 (0.33), residues: 239 loop : 0.23 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.024 0.001 TYR R 148 ARG 0.004 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.0851 (tmm) cc_final: 0.0572 (tmm) REVERT: B 59 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: G 42 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: G 47 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: N 19 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7586 (ttt180) REVERT: R 110 TRP cc_start: 0.4358 (m100) cc_final: 0.4062 (m100) REVERT: R 336 LYS cc_start: 0.7755 (mmtp) cc_final: 0.7546 (mmtm) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 1.6790 time to fit residues: 211.2979 Evaluate side-chains 119 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 301 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 0.0000 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10379 Z= 0.198 Angle : 0.712 37.224 14086 Z= 0.323 Chirality : 0.042 0.149 1542 Planarity : 0.004 0.051 1793 Dihedral : 6.429 96.620 1394 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.56 % Allowed : 15.05 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.24), residues: 1240 helix: 1.44 (0.23), residues: 525 sheet: 0.34 (0.33), residues: 239 loop : 0.25 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.023 0.002 TYR R 148 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.0752 (tmm) cc_final: 0.0461 (tmm) REVERT: B 59 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: G 42 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: N 19 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7578 (ttt180) REVERT: R 110 TRP cc_start: 0.4360 (m100) cc_final: 0.4065 (m100) REVERT: R 336 LYS cc_start: 0.7765 (mmtp) cc_final: 0.7552 (mmtm) outliers start: 17 outliers final: 7 residues processed: 121 average time/residue: 1.6863 time to fit residues: 215.6107 Evaluate side-chains 119 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN B 16 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10379 Z= 0.154 Angle : 0.687 37.427 14086 Z= 0.308 Chirality : 0.041 0.170 1542 Planarity : 0.004 0.052 1793 Dihedral : 6.266 95.825 1394 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.01 % Allowed : 15.50 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.24), residues: 1240 helix: 1.55 (0.23), residues: 522 sheet: 0.39 (0.33), residues: 238 loop : 0.25 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.023 0.001 TYR R 148 ARG 0.010 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.0832 (tmm) cc_final: 0.0546 (tmm) REVERT: B 59 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: G 42 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: N 19 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7532 (ttt180) REVERT: R 110 TRP cc_start: 0.4337 (m100) cc_final: 0.4056 (m100) REVERT: R 336 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7534 (mmtm) outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 1.5939 time to fit residues: 202.9603 Evaluate side-chains 120 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 88 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.166809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100887 restraints weight = 11757.523| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.10 r_work: 0.3109 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10379 Z= 0.258 Angle : 0.742 37.054 14086 Z= 0.341 Chirality : 0.044 0.144 1542 Planarity : 0.004 0.050 1793 Dihedral : 6.607 98.520 1394 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.19 % Allowed : 15.23 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1240 helix: 1.35 (0.22), residues: 522 sheet: 0.33 (0.33), residues: 239 loop : 0.25 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.002 PHE B 151 TYR 0.023 0.002 TYR R 148 ARG 0.006 0.000 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4812.59 seconds wall clock time: 85 minutes 13.49 seconds (5113.49 seconds total)