Starting phenix.real_space_refine on Tue Feb 13 17:11:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2024/7ld3_23280_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2024/7ld3_23280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2024/7ld3_23280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2024/7ld3_23280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2024/7ld3_23280_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2024/7ld3_23280_updated.pdb" } resolution = 3.2 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: 6 Type Number sf(0) Gaussians S 53 5.16 5 Cl 1 4.86 5 C 4498 2.51 5 N 1189 2.21 5 O 1269 1.98 5 F 6 1.80 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 TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G PHE 61": "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: 7016 Number of models: 1 Model: "" Number of chains: 5 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: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2273 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 14, 'TRANS': 273} Chain breaks: 1 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'ADN%rna3p': 1, 'XTD': 1} Classifications: {'undetermined': 2, 'water': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Time building chain proxies: 4.44, per 1000 atoms: 0.63 Number of scatterers: 7016 At special positions: 0 Unit cell: (127.204, 88.382, 102.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 53 16.00 F 6 9.00 O 1269 8.00 N 1189 7.00 C 4498 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=2.03 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 263 " distance=2.04 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: 2.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 9 sheets defined 42.2% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 12 through 29 Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.515A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) 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 removed outlier: 3.516A pdb=" N PHE A 216 " --> pdb=" O ILE A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.644A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.577A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 35 removed outlier: 3.759A pdb=" N ALA R 11 " --> pdb=" O ALA R 7 " (cutoff:3.500A) Proline residue: R 25 - end of helix Processing helix chain 'R' and resid 43 through 61 Processing helix chain 'R' and resid 63 through 71 Processing helix chain 'R' and resid 77 through 110 Proline residue: R 86 - end of helix Processing helix chain 'R' and resid 121 through 143 Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 148 through 159 removed outlier: 3.613A pdb=" N VAL R 152 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU R 153 " --> pdb=" O SER R 150 " (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 removed outlier: 3.585A pdb=" N ASN R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 259 Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 267 through 280 Processing helix chain 'R' and resid 284 through 287 No H-bonds generated for 'chain 'R' and resid 284 through 287' Processing helix chain 'R' and resid 293 through 299 Processing helix chain 'B' and resid 5 through 24 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 24 removed outlier: 3.778A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (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 sheet with id= A, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.995A pdb=" N ILE A 265 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N HIS A 323 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 267 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A 38 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY A 40 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 74 through 76 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.939A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.027A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.649A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.816A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.626A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.543A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.505A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 942 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: 1.86 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1636 1.33 - 1.45: 1604 1.45 - 1.58: 3841 1.58 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 7159 Sorted by residual: bond pdb=" C VAL R 24 " pdb=" N PRO R 25 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.69e+00 bond pdb=" CA ILE G 28 " pdb=" CB ILE G 28 " ideal model delta sigma weight residual 1.547 1.577 -0.030 1.68e-02 3.54e+03 3.29e+00 bond pdb=" C XTD R 402 " pdb=" C7 XTD R 402 " ideal model delta sigma weight residual 1.448 1.483 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.92e+00 bond pdb=" CB PRO R 142 " pdb=" CG PRO R 142 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.80e+00 ... (remaining 7154 not shown) Histogram of bond angle deviations from ideal: 91.06 - 99.79: 3 99.79 - 108.51: 431 108.51 - 117.24: 4653 117.24 - 125.96: 4483 125.96 - 134.69: 134 Bond angle restraints: 9704 Sorted by residual: angle pdb=" CA CYS R 263 " pdb=" CB CYS R 263 " pdb=" SG CYS R 263 " ideal model delta sigma weight residual 114.40 124.77 -10.37 2.30e+00 1.89e-01 2.03e+01 angle pdb=" CA ILE G 28 " pdb=" CB ILE G 28 " pdb=" CG2 ILE G 28 " ideal model delta sigma weight residual 110.50 117.83 -7.33 1.70e+00 3.46e-01 1.86e+01 angle pdb=" CA CYS R 260 " pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " ideal model delta sigma weight residual 114.40 123.83 -9.43 2.30e+00 1.89e-01 1.68e+01 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 129.94 -13.64 3.50e+00 8.16e-02 1.52e+01 angle pdb=" CA LYS G 29 " pdb=" CB LYS G 29 " pdb=" CG LYS G 29 " ideal model delta sigma weight residual 114.10 106.36 7.74 2.00e+00 2.50e-01 1.50e+01 ... (remaining 9699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3900 16.42 - 32.84: 305 32.84 - 49.26: 71 49.26 - 65.68: 13 65.68 - 82.11: 4 Dihedral angle restraints: 4293 sinusoidal: 1703 harmonic: 2590 Sorted by residual: dihedral pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -43.23 -42.77 1 1.00e+01 1.00e-02 2.55e+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 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLN R 74 " pdb=" C GLN R 74 " pdb=" N THR R 75 " pdb=" CA THR R 75 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1028 0.112 - 0.224: 88 0.224 - 0.337: 1 0.337 - 0.449: 0 0.449 - 0.561: 1 Chirality restraints: 1118 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 -2.07 -0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CB ILE G 9 " pdb=" CA ILE G 9 " pdb=" CG1 ILE G 9 " pdb=" CG2 ILE G 9 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE G 28 " pdb=" CA ILE G 28 " pdb=" CG1 ILE G 28 " pdb=" CG2 ILE G 28 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1115 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 XTD R 402 " -0.047 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" C11 XTD R 402 " 0.023 2.00e-02 2.50e+03 pdb=" C12 XTD R 402 " 0.029 2.00e-02 2.50e+03 pdb=" C13 XTD R 402 " 0.015 2.00e-02 2.50e+03 pdb=" C14 XTD R 402 " -0.037 2.00e-02 2.50e+03 pdb=" C15 XTD R 402 " 0.014 2.00e-02 2.50e+03 pdb=" C16 XTD R 402 " 0.013 2.00e-02 2.50e+03 pdb=" C17 XTD R 402 " -0.035 2.00e-02 2.50e+03 pdb=" C18 XTD R 402 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADN R 401 " -0.059 2.00e-02 2.50e+03 2.45e-02 1.65e+01 pdb=" C2 ADN R 401 " 0.008 2.00e-02 2.50e+03 pdb=" C4 ADN R 401 " 0.016 2.00e-02 2.50e+03 pdb=" C5 ADN R 401 " 0.012 2.00e-02 2.50e+03 pdb=" C6 ADN R 401 " -0.010 2.00e-02 2.50e+03 pdb=" C8 ADN R 401 " 0.020 2.00e-02 2.50e+03 pdb=" N1 ADN R 401 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ADN R 401 " 0.022 2.00e-02 2.50e+03 pdb=" N6 ADN R 401 " -0.035 2.00e-02 2.50e+03 pdb=" N7 ADN R 401 " 0.016 2.00e-02 2.50e+03 pdb=" N9 ADN R 401 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 173 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C THR B 173 " 0.063 2.00e-02 2.50e+03 pdb=" O THR B 173 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY B 174 " -0.022 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1770 2.80 - 3.33: 6369 3.33 - 3.85: 11818 3.85 - 4.38: 14233 4.38 - 4.90: 24302 Nonbonded interactions: 58492 Sorted by model distance: nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.277 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.295 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.312 2.440 nonbonded pdb=" O VAL R 138 " pdb=" OH TYR R 179 " model vdw 2.319 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.322 2.440 ... (remaining 58487 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: 0.860 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: 3.780 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.770 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.006 0.084 7159 Z= 0.401 Angle : 1.018 13.637 9704 Z= 0.566 Chirality : 0.063 0.561 1118 Planarity : 0.008 0.087 1211 Dihedral : 12.923 82.106 2603 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.04 % 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: -1.50 (0.25), residues: 872 helix: -1.42 (0.22), residues: 404 sheet: 0.84 (0.38), residues: 173 loop : -1.24 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 99 HIS 0.006 0.002 HIS A 323 PHE 0.042 0.003 PHE R 275 TYR 0.033 0.003 TYR A 297 ARG 0.012 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8398 (m-80) cc_final: 0.7763 (m-80) REVERT: B 259 GLN cc_start: 0.8285 (pt0) cc_final: 0.7913 (pt0) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2036 time to fit residues: 32.6963 Evaluate side-chains 76 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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: 2.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 332 ASN B 91 HIS B 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7159 Z= 0.209 Angle : 0.557 8.003 9704 Z= 0.298 Chirality : 0.042 0.172 1118 Planarity : 0.005 0.063 1211 Dihedral : 7.020 57.741 995 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.32 % Allowed : 9.11 % Favored : 89.56 % 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: -0.14 (0.27), residues: 872 helix: 0.26 (0.25), residues: 406 sheet: 0.68 (0.37), residues: 173 loop : -0.93 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS R 251 PHE 0.036 0.001 PHE R 275 TYR 0.012 0.001 TYR B 124 ARG 0.003 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7733 (ptt-90) cc_final: 0.7381 (ptp-170) REVERT: A 208 GLU cc_start: 0.7930 (pt0) cc_final: 0.7646 (pt0) REVERT: A 210 LYS cc_start: 0.9024 (ptmt) cc_final: 0.8484 (pttt) REVERT: B 101 MET cc_start: 0.8786 (mtp) cc_final: 0.8388 (mtp) REVERT: B 146 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7812 (mp) REVERT: B 175 GLN cc_start: 0.8066 (mp10) cc_final: 0.7815 (mp10) REVERT: B 197 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7680 (mtp85) REVERT: B 228 ASP cc_start: 0.8108 (m-30) cc_final: 0.7810 (m-30) outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 0.1895 time to fit residues: 24.0543 Evaluate side-chains 84 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7159 Z= 0.369 Angle : 0.584 7.263 9704 Z= 0.310 Chirality : 0.045 0.180 1118 Planarity : 0.005 0.063 1211 Dihedral : 6.739 58.235 995 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.64 % Allowed : 10.70 % Favored : 86.66 % 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: 0.02 (0.28), residues: 872 helix: 0.70 (0.26), residues: 398 sheet: 0.17 (0.36), residues: 183 loop : -0.91 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS R 251 PHE 0.031 0.002 PHE R 275 TYR 0.009 0.001 TYR B 85 ARG 0.002 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.774 Fit side-chains REVERT: A 32 ARG cc_start: 0.7896 (ptt-90) cc_final: 0.7451 (ptp-170) REVERT: A 208 GLU cc_start: 0.7998 (pt0) cc_final: 0.7416 (pt0) REVERT: A 210 LYS cc_start: 0.8989 (ptmt) cc_final: 0.8347 (pttm) REVERT: B 101 MET cc_start: 0.8831 (mtp) cc_final: 0.8428 (mtp) REVERT: B 146 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7910 (mp) outliers start: 20 outliers final: 11 residues processed: 102 average time/residue: 0.2056 time to fit residues: 28.0520 Evaluate side-chains 86 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.0570 chunk 59 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7159 Z= 0.208 Angle : 0.502 6.836 9704 Z= 0.266 Chirality : 0.042 0.167 1118 Planarity : 0.004 0.054 1211 Dihedral : 6.239 56.532 995 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.64 % Allowed : 12.42 % Favored : 84.94 % 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: 0.16 (0.28), residues: 872 helix: 0.98 (0.27), residues: 400 sheet: -0.05 (0.36), residues: 166 loop : -0.88 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 251 PHE 0.031 0.001 PHE R 275 TYR 0.008 0.001 TYR B 124 ARG 0.002 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.826 Fit side-chains REVERT: A 32 ARG cc_start: 0.7834 (ptt-90) cc_final: 0.7499 (ptp-170) REVERT: A 187 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: A 208 GLU cc_start: 0.7932 (pt0) cc_final: 0.7638 (pt0) REVERT: A 210 LYS cc_start: 0.9001 (ptmt) cc_final: 0.8427 (pttt) REVERT: B 321 THR cc_start: 0.8404 (p) cc_final: 0.8167 (p) outliers start: 20 outliers final: 10 residues processed: 87 average time/residue: 0.1941 time to fit residues: 22.8728 Evaluate side-chains 81 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 71 optimal weight: 0.0980 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7159 Z= 0.165 Angle : 0.479 6.635 9704 Z= 0.253 Chirality : 0.041 0.159 1118 Planarity : 0.004 0.049 1211 Dihedral : 5.803 52.953 995 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.59 % Allowed : 14.53 % Favored : 83.88 % 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: 0.35 (0.28), residues: 872 helix: 1.21 (0.27), residues: 400 sheet: 0.03 (0.37), residues: 166 loop : -0.87 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 251 PHE 0.029 0.001 PHE R 275 TYR 0.007 0.001 TYR B 124 ARG 0.002 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.683 Fit side-chains REVERT: A 187 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: A 296 LYS cc_start: 0.7951 (mppt) cc_final: 0.7694 (mmtt) REVERT: B 101 MET cc_start: 0.8717 (mtp) cc_final: 0.8447 (mtp) REVERT: B 321 THR cc_start: 0.8438 (p) cc_final: 0.8208 (p) REVERT: G 28 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7581 (tt) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.2100 time to fit residues: 22.7263 Evaluate side-chains 75 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET 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: 5.9990 chunk 20 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7159 Z= 0.266 Angle : 0.520 6.557 9704 Z= 0.275 Chirality : 0.043 0.159 1118 Planarity : 0.004 0.050 1211 Dihedral : 5.886 52.620 995 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.64 % Allowed : 14.13 % Favored : 83.22 % 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: 0.26 (0.28), residues: 872 helix: 1.09 (0.27), residues: 408 sheet: -0.08 (0.37), residues: 166 loop : -0.87 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 251 PHE 0.027 0.001 PHE R 275 TYR 0.009 0.001 TYR B 111 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 70 time to evaluate : 0.795 Fit side-chains REVERT: A 187 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: A 296 LYS cc_start: 0.8006 (mppt) cc_final: 0.7690 (mmtt) REVERT: B 101 MET cc_start: 0.8768 (mtp) cc_final: 0.8502 (mtp) REVERT: B 197 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7639 (mtp85) REVERT: G 28 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7559 (tt) outliers start: 20 outliers final: 11 residues processed: 85 average time/residue: 0.1928 time to fit residues: 22.5088 Evaluate side-chains 77 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7159 Z= 0.257 Angle : 0.523 8.863 9704 Z= 0.274 Chirality : 0.042 0.151 1118 Planarity : 0.004 0.049 1211 Dihedral : 5.910 52.188 995 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.04 % Allowed : 14.27 % Favored : 82.69 % 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: 0.21 (0.29), residues: 872 helix: 1.12 (0.27), residues: 408 sheet: -0.32 (0.37), residues: 170 loop : -0.86 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 251 PHE 0.026 0.001 PHE R 275 TYR 0.010 0.001 TYR B 111 ARG 0.001 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.903 Fit side-chains REVERT: A 187 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: A 277 GLU cc_start: 0.7488 (tp30) cc_final: 0.7119 (tp30) REVERT: A 296 LYS cc_start: 0.8022 (mppt) cc_final: 0.7683 (mmtt) REVERT: B 45 MET cc_start: 0.8152 (mtt) cc_final: 0.7868 (mtt) REVERT: B 55 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8633 (mt) REVERT: B 101 MET cc_start: 0.8823 (mtp) cc_final: 0.8528 (mtp) REVERT: B 197 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7606 (mtp85) REVERT: G 28 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7571 (tt) outliers start: 23 outliers final: 13 residues processed: 90 average time/residue: 0.1861 time to fit residues: 23.0174 Evaluate side-chains 84 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7159 Z= 0.204 Angle : 0.496 7.852 9704 Z= 0.261 Chirality : 0.041 0.142 1118 Planarity : 0.004 0.048 1211 Dihedral : 5.704 50.817 995 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.64 % Allowed : 14.93 % Favored : 82.43 % 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: 0.36 (0.29), residues: 872 helix: 1.29 (0.27), residues: 405 sheet: -0.30 (0.37), residues: 170 loop : -0.80 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 251 PHE 0.025 0.001 PHE R 275 TYR 0.010 0.001 TYR B 111 ARG 0.001 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 70 time to evaluate : 0.763 Fit side-chains REVERT: A 51 LYS cc_start: 0.8728 (mptt) cc_final: 0.8485 (mmtt) REVERT: A 187 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7015 (mt-10) REVERT: A 277 GLU cc_start: 0.7585 (tp30) cc_final: 0.7274 (tp30) REVERT: A 296 LYS cc_start: 0.8024 (mppt) cc_final: 0.7755 (mmtt) REVERT: B 55 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8585 (mt) REVERT: B 101 MET cc_start: 0.8832 (mtp) cc_final: 0.8492 (mtp) REVERT: B 197 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7639 (mtp85) REVERT: G 28 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7523 (tt) outliers start: 20 outliers final: 14 residues processed: 85 average time/residue: 0.1816 time to fit residues: 21.4694 Evaluate side-chains 84 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7159 Z= 0.250 Angle : 0.519 8.025 9704 Z= 0.271 Chirality : 0.042 0.143 1118 Planarity : 0.004 0.048 1211 Dihedral : 5.678 49.187 995 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.38 % Allowed : 15.59 % Favored : 82.03 % 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: 0.27 (0.29), residues: 872 helix: 1.16 (0.27), residues: 411 sheet: -0.37 (0.36), residues: 175 loop : -0.80 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 251 PHE 0.024 0.001 PHE R 275 TYR 0.010 0.001 TYR B 111 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.714 Fit side-chains REVERT: A 277 GLU cc_start: 0.7678 (tp30) cc_final: 0.7397 (tp30) REVERT: A 296 LYS cc_start: 0.8028 (mppt) cc_final: 0.7740 (mmtt) REVERT: B 55 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8542 (mt) REVERT: B 101 MET cc_start: 0.8839 (mtp) cc_final: 0.8525 (mtp) REVERT: B 197 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7666 (mtp85) REVERT: G 28 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7577 (tt) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.1821 time to fit residues: 21.1940 Evaluate side-chains 84 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7159 Z= 0.192 Angle : 0.498 7.695 9704 Z= 0.260 Chirality : 0.041 0.137 1118 Planarity : 0.004 0.047 1211 Dihedral : 5.513 48.445 995 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.25 % Allowed : 15.98 % Favored : 81.77 % 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: 0.46 (0.29), residues: 872 helix: 1.33 (0.27), residues: 407 sheet: -0.31 (0.36), residues: 175 loop : -0.66 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS R 251 PHE 0.024 0.001 PHE R 275 TYR 0.009 0.001 TYR B 111 ARG 0.001 0.000 ARG R 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 0.833 Fit side-chains REVERT: A 277 GLU cc_start: 0.7765 (tp30) cc_final: 0.7508 (tp30) REVERT: A 296 LYS cc_start: 0.8009 (mppt) cc_final: 0.7731 (mmtt) REVERT: B 55 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8512 (mt) REVERT: B 101 MET cc_start: 0.8822 (mtp) cc_final: 0.8477 (mtp) REVERT: G 28 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7543 (tt) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.1997 time to fit residues: 22.3242 Evaluate side-chains 81 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.165736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134690 restraints weight = 7570.388| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.66 r_work: 0.3337 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7159 Z= 0.191 Angle : 0.500 7.649 9704 Z= 0.260 Chirality : 0.041 0.136 1118 Planarity : 0.004 0.047 1211 Dihedral : 5.452 48.553 995 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.25 % Allowed : 15.85 % Favored : 81.90 % 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: 0.54 (0.29), residues: 872 helix: 1.40 (0.27), residues: 407 sheet: -0.29 (0.36), residues: 175 loop : -0.61 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS R 251 PHE 0.023 0.001 PHE R 275 TYR 0.009 0.001 TYR B 111 ARG 0.002 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1786.16 seconds wall clock time: 33 minutes 21.23 seconds (2001.23 seconds total)