Starting phenix.real_space_refine on Tue Feb 13 16:53:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld4_23281/02_2024/7ld4_23281_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld4_23281/02_2024/7ld4_23281.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/7ld4_23281/02_2024/7ld4_23281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld4_23281/02_2024/7ld4_23281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld4_23281/02_2024/7ld4_23281_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld4_23281/02_2024/7ld4_23281_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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4476 2.51 5 N 1187 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 208": "OE1" <-> "OE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 42": "OD1" <-> "OD2" Residue "R ASP 55": "OD1" <-> "OD2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6981 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1693 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 207} Chain breaks: 2 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2568 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2287 Unusual residues: {'ADN%rna2p': 1} Classifications: {'peptide': 287, 'undetermined': 1, 'water': 1} Modifications used: {'rna2p': 1} Link IDs: {'PTRANS': 14, 'TRANS': 272, None: 2} Not linked: pdbres="LYS R 301 " pdbres="ADN R 401 " Not linked: pdbres="ADN R 401 " pdbres="HOH R 501 " Chain breaks: 1 Time building chain proxies: 4.27, per 1000 atoms: 0.61 Number of scatterers: 6981 At special positions: 0 Unit cell: (82.68, 125.08, 90.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1266 8.00 N 1187 7.00 C 4476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 80 " - pdb=" SG CYS R 169 " distance=2.00 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 263 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1682 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 9 sheets defined 42.5% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 12 through 29 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.816A pdb=" N LEU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.531A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.588A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (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: 3.884A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.521A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 7 through 36 Proline residue: R 25 - end of helix Processing helix chain 'R' and resid 43 through 60 removed outlier: 3.593A pdb=" N PHE R 47 " --> pdb=" O ALA R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 71 Processing helix chain 'R' and resid 77 through 110 Proline residue: R 86 - end of helix removed outlier: 4.201A pdb=" N VAL R 109 " --> pdb=" O ARG R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 118 No H-bonds generated for 'chain 'R' and resid 115 through 118' Processing helix chain 'R' and resid 121 through 140 removed outlier: 3.540A pdb=" N VAL R 126 " --> pdb=" O ARG R 122 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL R 138 " --> pdb=" O LEU R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 159 removed outlier: 3.698A pdb=" N ARG R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 174 No H-bonds generated for 'chain 'R' and resid 171 through 174' Processing helix chain 'R' and resid 177 through 182 Processing helix chain 'R' and resid 185 through 188 No H-bonds generated for 'chain 'R' and resid 185 through 188' Processing helix chain 'R' and resid 190 through 212 Processing helix chain 'R' and resid 226 through 258 removed outlier: 3.979A pdb=" N LEU R 248 " --> pdb=" O ALA R 244 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 267 through 287 removed outlier: 4.536A pdb=" N SER R 281 " --> pdb=" O THR R 277 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA R 282 " --> pdb=" O HIS R 278 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 293 through 300 removed outlier: 3.679A pdb=" N THR R 298 " --> pdb=" O LYS R 294 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE R 299 " --> pdb=" O PHE R 295 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 320 through 324 removed outlier: 7.176A pdb=" N ILE A 265 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N HIS A 323 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 267 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU A 38 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLY A 40 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.891A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.608A 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: 6.956A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.034A 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: 6.695A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.833A 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: 6.648A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.213A 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: 6.603A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.930A 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: 6.464A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.432A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 74 through 76 317 hydrogen bonds defined for protein. 927 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: 1.83 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2170 1.34 - 1.46: 1309 1.46 - 1.58: 3568 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 7122 Sorted by residual: bond pdb=" CB VAL R 62 " pdb=" CG2 VAL R 62 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.23e+00 bond pdb=" CB VAL R 119 " pdb=" CG1 VAL R 119 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" C VAL R 24 " pdb=" N PRO R 25 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.12e+00 bond pdb=" CB VAL R 83 " pdb=" CG2 VAL R 83 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 ... (remaining 7117 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.76: 119 105.76 - 113.55: 3949 113.55 - 121.34: 3770 121.34 - 129.14: 1743 129.14 - 136.93: 67 Bond angle restraints: 9648 Sorted by residual: angle pdb=" CA CYS R 169 " pdb=" CB CYS R 169 " pdb=" SG CYS R 169 " ideal model delta sigma weight residual 114.40 97.97 16.43 2.30e+00 1.89e-01 5.10e+01 angle pdb=" CA LEU R 68 " pdb=" CB LEU R 68 " pdb=" CG LEU R 68 " ideal model delta sigma weight residual 116.30 136.93 -20.63 3.50e+00 8.16e-02 3.47e+01 angle pdb=" N GLY R 72 " pdb=" CA GLY R 72 " pdb=" C GLY R 72 " ideal model delta sigma weight residual 112.34 124.06 -11.72 2.04e+00 2.40e-01 3.30e+01 angle pdb=" N VAL R 119 " pdb=" CA VAL R 119 " pdb=" C VAL R 119 " ideal model delta sigma weight residual 106.21 111.35 -5.14 1.07e+00 8.73e-01 2.31e+01 angle pdb=" CA LEU R 18 " pdb=" CB LEU R 18 " pdb=" CG LEU R 18 " ideal model delta sigma weight residual 116.30 130.57 -14.27 3.50e+00 8.16e-02 1.66e+01 ... (remaining 9643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 3904 16.44 - 32.87: 282 32.87 - 49.31: 64 49.31 - 65.75: 10 65.75 - 82.18: 5 Dihedral angle restraints: 4265 sinusoidal: 1678 harmonic: 2587 Sorted by residual: dihedral pdb=" C1' ADN R 401 " pdb=" C2' ADN R 401 " pdb=" C3' ADN R 401 " pdb=" C4' ADN R 401 " ideal model delta sinusoidal sigma weight residual -35.00 6.27 -41.27 1 8.00e+00 1.56e-02 3.73e+01 dihedral pdb=" C2' ADN R 401 " pdb=" C3' ADN R 401 " pdb=" C4' ADN R 401 " pdb=" O4' ADN R 401 " ideal model delta sinusoidal sigma weight residual 24.00 -13.82 37.82 1 8.00e+00 1.56e-02 3.15e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 4262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 918 0.088 - 0.176: 179 0.176 - 0.264: 16 0.264 - 0.352: 3 0.352 - 0.440: 1 Chirality restraints: 1117 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CB VAL R 119 " pdb=" CA VAL R 119 " pdb=" CG1 VAL R 119 " pdb=" CG2 VAL R 119 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL R 83 " pdb=" CA VAL R 83 " pdb=" CG1 VAL R 83 " pdb=" CG2 VAL R 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1114 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 275 " 0.029 2.00e-02 2.50e+03 3.00e-02 1.58e+01 pdb=" CG PHE R 275 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE R 275 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE R 275 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 275 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 275 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 275 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADN R 401 " 0.010 2.00e-02 2.50e+03 2.02e-02 1.12e+01 pdb=" C2 ADN R 401 " 0.018 2.00e-02 2.50e+03 pdb=" C4 ADN R 401 " -0.033 2.00e-02 2.50e+03 pdb=" C5 ADN R 401 " -0.022 2.00e-02 2.50e+03 pdb=" C6 ADN R 401 " 0.004 2.00e-02 2.50e+03 pdb=" C8 ADN R 401 " 0.025 2.00e-02 2.50e+03 pdb=" N1 ADN R 401 " 0.029 2.00e-02 2.50e+03 pdb=" N3 ADN R 401 " -0.015 2.00e-02 2.50e+03 pdb=" N6 ADN R 401 " -0.018 2.00e-02 2.50e+03 pdb=" N7 ADN R 401 " 0.015 2.00e-02 2.50e+03 pdb=" N9 ADN R 401 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 22 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C VAL R 22 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL R 22 " 0.018 2.00e-02 2.50e+03 pdb=" N SER R 23 " 0.017 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1697 2.80 - 3.32: 6408 3.32 - 3.85: 11525 3.85 - 4.37: 13698 4.37 - 4.90: 23621 Nonbonded interactions: 56949 Sorted by model distance: nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.284 2.440 nonbonded pdb=" OE2 GLU A 319 " pdb=" OH TYR A 321 " model vdw 2.294 2.440 nonbonded pdb=" O SER R 23 " pdb=" ND2 ASN R 27 " model vdw 2.340 2.520 nonbonded pdb=" O LEU R 90 " pdb=" OG SER R 93 " model vdw 2.340 2.440 ... (remaining 56944 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.600 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.850 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.008 0.075 7122 Z= 0.537 Angle : 1.119 20.629 9648 Z= 0.616 Chirality : 0.070 0.440 1117 Planarity : 0.008 0.052 1206 Dihedral : 12.683 82.182 2577 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.26 % Allowed : 4.37 % Favored : 95.37 % 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: -0.88 (0.27), residues: 871 helix: -0.83 (0.24), residues: 401 sheet: 0.82 (0.40), residues: 167 loop : -0.79 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP R 247 HIS 0.011 0.002 HIS A 281 PHE 0.070 0.004 PHE R 275 TYR 0.038 0.004 TYR R 179 ARG 0.020 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7365 (tpt-90) cc_final: 0.7091 (ttm-80) REVERT: A 21 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7672 (tttp) REVERT: A 342 ASP cc_start: 0.7880 (m-30) cc_final: 0.7614 (m-30) REVERT: B 120 ILE cc_start: 0.9125 (mm) cc_final: 0.8922 (mm) REVERT: B 275 SER cc_start: 0.9031 (m) cc_final: 0.8821 (m) REVERT: R 74 GLN cc_start: 0.8331 (mt0) cc_final: 0.8036 (mp10) REVERT: R 76 TYR cc_start: 0.8135 (m-80) cc_final: 0.7843 (m-10) REVERT: R 162 MET cc_start: 0.6158 (mmt) cc_final: 0.5497 (mmt) REVERT: R 234 LYS cc_start: 0.7650 (mtpt) cc_final: 0.6674 (tttp) REVERT: R 288 TYR cc_start: 0.9280 (m-80) cc_final: 0.9001 (m-80) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.3085 time to fit residues: 57.4476 Evaluate side-chains 112 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 132 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7122 Z= 0.194 Angle : 0.560 9.297 9648 Z= 0.298 Chirality : 0.044 0.233 1117 Planarity : 0.005 0.046 1206 Dihedral : 7.777 66.195 970 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.46 % Allowed : 10.45 % Favored : 88.10 % 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: 0.20 (0.28), residues: 871 helix: 0.44 (0.25), residues: 417 sheet: 0.82 (0.38), residues: 172 loop : -0.58 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.003 0.001 HIS R 251 PHE 0.035 0.002 PHE R 275 TYR 0.015 0.001 TYR B 124 ARG 0.006 0.000 ARG R 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.728 Fit side-chains REVERT: A 21 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7568 (tttp) REVERT: A 28 GLU cc_start: 0.7283 (pp20) cc_final: 0.6976 (pp20) REVERT: B 120 ILE cc_start: 0.9154 (mm) cc_final: 0.8950 (mm) REVERT: B 258 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7408 (m-30) REVERT: B 297 TRP cc_start: 0.8632 (m100) cc_final: 0.8354 (m100) REVERT: R 74 GLN cc_start: 0.8183 (mt0) cc_final: 0.7947 (mp10) REVERT: R 76 TYR cc_start: 0.8156 (m-80) cc_final: 0.7808 (m-10) REVERT: R 275 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7744 (p90) outliers start: 11 outliers final: 6 residues processed: 135 average time/residue: 0.2712 time to fit residues: 45.2825 Evaluate side-chains 114 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 281 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 295 ASN B 132 ASN R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7122 Z= 0.203 Angle : 0.528 8.147 9648 Z= 0.281 Chirality : 0.043 0.223 1117 Planarity : 0.004 0.046 1206 Dihedral : 7.464 63.860 970 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.72 % Allowed : 13.23 % Favored : 85.05 % 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: 0.49 (0.28), residues: 871 helix: 0.82 (0.26), residues: 417 sheet: 0.55 (0.37), residues: 182 loop : -0.43 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 PHE 0.029 0.001 PHE R 275 TYR 0.010 0.001 TYR R 288 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.784 Fit side-chains REVERT: A 21 LYS cc_start: 0.7884 (ttpp) cc_final: 0.7562 (tttp) REVERT: B 258 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: G 40 TYR cc_start: 0.8276 (t80) cc_final: 0.7864 (t80) REVERT: R 74 GLN cc_start: 0.8199 (mt0) cc_final: 0.7985 (mp10) REVERT: R 76 TYR cc_start: 0.8406 (m-80) cc_final: 0.8154 (m-10) outliers start: 13 outliers final: 8 residues processed: 119 average time/residue: 0.2587 time to fit residues: 38.6111 Evaluate side-chains 115 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 83 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 0.0470 chunk 53 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 132 ASN R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7122 Z= 0.295 Angle : 0.564 7.368 9648 Z= 0.301 Chirality : 0.044 0.225 1117 Planarity : 0.004 0.050 1206 Dihedral : 7.522 63.541 970 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.04 % Allowed : 13.62 % Favored : 83.33 % 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: 0.49 (0.28), residues: 871 helix: 0.85 (0.26), residues: 417 sheet: 0.51 (0.38), residues: 182 loop : -0.46 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.029 0.002 PHE R 275 TYR 0.009 0.001 TYR R 288 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.864 Fit side-chains REVERT: A 241 MET cc_start: 0.4441 (ttm) cc_final: 0.3607 (tpt) REVERT: B 25 CYS cc_start: 0.7507 (p) cc_final: 0.7281 (p) REVERT: B 217 MET cc_start: 0.7170 (mmm) cc_final: 0.6808 (mmm) REVERT: G 40 TYR cc_start: 0.8320 (t80) cc_final: 0.7895 (t80) REVERT: R 74 GLN cc_start: 0.8272 (mt0) cc_final: 0.8028 (mp10) REVERT: R 275 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7544 (p90) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.2526 time to fit residues: 37.4957 Evaluate side-chains 118 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7122 Z= 0.146 Angle : 0.494 6.984 9648 Z= 0.263 Chirality : 0.041 0.220 1117 Planarity : 0.004 0.046 1206 Dihedral : 7.348 64.316 970 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.78 % Allowed : 13.36 % Favored : 83.86 % 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 (0.29), residues: 871 helix: 1.05 (0.26), residues: 422 sheet: 0.53 (0.39), residues: 181 loop : -0.46 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 264 PHE 0.023 0.001 PHE R 275 TYR 0.008 0.001 TYR B 124 ARG 0.008 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.763 Fit side-chains REVERT: A 52 GLN cc_start: 0.6899 (mt0) cc_final: 0.6382 (mp10) REVERT: A 241 MET cc_start: 0.4243 (ttm) cc_final: 0.3695 (tpt) REVERT: B 18 ILE cc_start: 0.7275 (mt) cc_final: 0.7068 (mt) REVERT: B 186 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.7840 (p0) REVERT: B 217 MET cc_start: 0.7084 (mmm) cc_final: 0.6608 (mmm) REVERT: B 258 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: G 40 TYR cc_start: 0.8283 (t80) cc_final: 0.7873 (t80) REVERT: R 74 GLN cc_start: 0.8198 (mt0) cc_final: 0.7828 (mp10) REVERT: R 275 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7323 (p90) outliers start: 21 outliers final: 11 residues processed: 125 average time/residue: 0.2301 time to fit residues: 37.1599 Evaluate side-chains 118 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 69 optimal weight: 0.4980 chunk 38 optimal weight: 0.0000 chunk 6 optimal weight: 0.0670 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN B 88 ASN B 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7122 Z= 0.131 Angle : 0.481 7.326 9648 Z= 0.254 Chirality : 0.041 0.204 1117 Planarity : 0.004 0.045 1206 Dihedral : 7.274 65.148 970 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.38 % Allowed : 15.21 % Favored : 82.41 % 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: 0.85 (0.29), residues: 871 helix: 1.25 (0.26), residues: 423 sheet: 0.74 (0.39), residues: 171 loop : -0.51 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 PHE 0.021 0.001 PHE R 275 TYR 0.008 0.001 TYR R 182 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.773 Fit side-chains REVERT: A 52 GLN cc_start: 0.6770 (mt0) cc_final: 0.6328 (mp10) REVERT: A 241 MET cc_start: 0.4175 (ttm) cc_final: 0.3729 (tpt) REVERT: B 18 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6996 (mt) REVERT: B 136 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7847 (t) REVERT: B 186 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.7915 (p0) REVERT: B 217 MET cc_start: 0.7072 (mmm) cc_final: 0.6749 (mmm) REVERT: B 258 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: B 297 TRP cc_start: 0.8528 (m100) cc_final: 0.7954 (m100) REVERT: R 74 GLN cc_start: 0.8147 (mt0) cc_final: 0.7823 (mp10) REVERT: R 275 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7210 (p90) outliers start: 18 outliers final: 9 residues processed: 117 average time/residue: 0.2223 time to fit residues: 33.5394 Evaluate side-chains 118 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7122 Z= 0.178 Angle : 0.499 9.717 9648 Z= 0.260 Chirality : 0.042 0.199 1117 Planarity : 0.004 0.047 1206 Dihedral : 7.292 65.044 970 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.17 % Allowed : 15.74 % Favored : 81.08 % 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: 0.84 (0.29), residues: 871 helix: 1.24 (0.26), residues: 424 sheet: 0.55 (0.39), residues: 176 loop : -0.40 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 251 PHE 0.021 0.001 PHE R 275 TYR 0.014 0.001 TYR G 40 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.823 Fit side-chains REVERT: A 52 GLN cc_start: 0.6797 (mt0) cc_final: 0.6346 (mp10) REVERT: A 241 MET cc_start: 0.4051 (OUTLIER) cc_final: 0.3634 (tpt) REVERT: B 18 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6995 (mt) REVERT: B 186 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.7891 (p0) REVERT: B 217 MET cc_start: 0.7121 (mmm) cc_final: 0.6814 (mmm) REVERT: B 258 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: B 297 TRP cc_start: 0.8554 (m100) cc_final: 0.7896 (m100) REVERT: G 40 TYR cc_start: 0.8253 (t80) cc_final: 0.7977 (t80) REVERT: R 74 GLN cc_start: 0.8181 (mt0) cc_final: 0.7874 (mp10) REVERT: R 275 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7188 (p90) outliers start: 24 outliers final: 16 residues processed: 118 average time/residue: 0.2177 time to fit residues: 33.3205 Evaluate side-chains 124 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7122 Z= 0.144 Angle : 0.489 8.923 9648 Z= 0.254 Chirality : 0.041 0.190 1117 Planarity : 0.004 0.046 1206 Dihedral : 7.255 65.246 970 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.65 % Allowed : 16.80 % Favored : 80.56 % 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 (0.29), residues: 871 helix: 1.33 (0.26), residues: 424 sheet: 0.63 (0.40), residues: 171 loop : -0.42 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS R 264 PHE 0.020 0.001 PHE R 275 TYR 0.012 0.001 TYR G 40 ARG 0.004 0.000 ARG R 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.885 Fit side-chains REVERT: A 52 GLN cc_start: 0.6764 (mt0) cc_final: 0.6322 (mp10) REVERT: A 241 MET cc_start: 0.4090 (OUTLIER) cc_final: 0.3660 (tpt) REVERT: A 346 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8124 (mptt) REVERT: B 18 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6953 (mt) REVERT: B 186 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.7898 (p0) REVERT: B 217 MET cc_start: 0.7113 (mmm) cc_final: 0.6827 (mmm) REVERT: B 258 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: B 297 TRP cc_start: 0.8514 (m100) cc_final: 0.7950 (m100) REVERT: G 40 TYR cc_start: 0.8229 (t80) cc_final: 0.7971 (t80) REVERT: R 74 GLN cc_start: 0.8149 (mt0) cc_final: 0.7871 (mp10) REVERT: R 275 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.6990 (p90) outliers start: 20 outliers final: 14 residues processed: 118 average time/residue: 0.2102 time to fit residues: 32.4465 Evaluate side-chains 125 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7122 Z= 0.172 Angle : 0.505 8.922 9648 Z= 0.262 Chirality : 0.042 0.186 1117 Planarity : 0.004 0.046 1206 Dihedral : 7.267 65.173 970 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.65 % Allowed : 17.20 % Favored : 80.16 % 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 (0.29), residues: 871 helix: 1.36 (0.26), residues: 421 sheet: 0.45 (0.39), residues: 176 loop : -0.35 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS R 251 PHE 0.020 0.001 PHE R 275 TYR 0.011 0.001 TYR G 40 ARG 0.004 0.000 ARG R 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.782 Fit side-chains REVERT: A 52 GLN cc_start: 0.6775 (mt0) cc_final: 0.6329 (mp10) REVERT: A 241 MET cc_start: 0.4104 (OUTLIER) cc_final: 0.3684 (tpt) REVERT: A 346 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8123 (mptt) REVERT: B 18 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6964 (mt) REVERT: B 186 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.7866 (p0) REVERT: B 217 MET cc_start: 0.7138 (mmm) cc_final: 0.6839 (mmm) REVERT: B 258 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: B 297 TRP cc_start: 0.8532 (m100) cc_final: 0.7921 (m100) REVERT: G 40 TYR cc_start: 0.8242 (t80) cc_final: 0.7992 (t80) REVERT: R 74 GLN cc_start: 0.8161 (mt0) cc_final: 0.7864 (mp10) REVERT: R 275 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.6991 (p90) outliers start: 20 outliers final: 14 residues processed: 117 average time/residue: 0.2145 time to fit residues: 32.6471 Evaluate side-chains 125 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7122 Z= 0.158 Angle : 0.501 8.910 9648 Z= 0.260 Chirality : 0.041 0.160 1117 Planarity : 0.004 0.046 1206 Dihedral : 7.236 65.193 970 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.65 % Allowed : 17.59 % Favored : 79.76 % 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: 0.93 (0.29), residues: 871 helix: 1.39 (0.26), residues: 421 sheet: 0.45 (0.39), residues: 176 loop : -0.36 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 245 PHE 0.019 0.001 PHE R 275 TYR 0.011 0.001 TYR G 40 ARG 0.005 0.000 ARG R 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.750 Fit side-chains REVERT: A 52 GLN cc_start: 0.6772 (mt0) cc_final: 0.6321 (mp10) REVERT: A 241 MET cc_start: 0.3926 (OUTLIER) cc_final: 0.3677 (tpt) REVERT: A 346 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8165 (mptt) REVERT: B 18 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6918 (mt) REVERT: B 186 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.7940 (p0) REVERT: B 217 MET cc_start: 0.7114 (mmm) cc_final: 0.6817 (mmm) REVERT: B 297 TRP cc_start: 0.8496 (m100) cc_final: 0.7928 (m100) REVERT: G 40 TYR cc_start: 0.8229 (t80) cc_final: 0.7990 (t80) REVERT: R 74 GLN cc_start: 0.8062 (mt0) cc_final: 0.7776 (mp10) REVERT: R 275 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.6953 (p90) outliers start: 20 outliers final: 15 residues processed: 111 average time/residue: 0.2077 time to fit residues: 30.1692 Evaluate side-chains 119 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.161170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141502 restraints weight = 8843.329| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.59 r_work: 0.3488 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7122 Z= 0.169 Angle : 0.510 8.876 9648 Z= 0.265 Chirality : 0.041 0.158 1117 Planarity : 0.004 0.046 1206 Dihedral : 7.240 65.184 970 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.91 % Allowed : 17.46 % Favored : 79.63 % 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: 0.93 (0.29), residues: 871 helix: 1.41 (0.26), residues: 421 sheet: 0.47 (0.40), residues: 173 loop : -0.39 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS R 251 PHE 0.020 0.001 PHE R 275 TYR 0.011 0.001 TYR G 40 ARG 0.005 0.000 ARG R 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1808.75 seconds wall clock time: 33 minutes 32.88 seconds (2012.88 seconds total)