Starting phenix.real_space_refine (version: dev) on Sat Feb 18 03:18:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2023/7ld3_23280_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2023/7ld3_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_2023/7ld3_23280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2023/7ld3_23280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2023/7ld3_23280_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ld3_23280/02_2023/7ld3_23280_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 4.53, per 1000 atoms: 0.65 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: 2.84 Conformation dependent library (CDL) restraints added in 814.5 milliseconds 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: 0.77 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: 2.29 Time building geometry restraints manager: 2.99 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: 3884 16.42 - 32.84: 299 32.84 - 49.26: 71 49.26 - 65.68: 9 65.68 - 82.11: 4 Dihedral angle restraints: 4267 sinusoidal: 1677 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 4264 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 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. 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.150 Check model and map are aligned: 0.090 Process input model: 22.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 12.702 82.106 2577 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 % 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 *********************** 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 : 0.835 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2296 time to fit residues: 36.7654 Evaluate side-chains 76 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.838 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1719 ------------------------------------------------------------------------------- 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: 2.9990 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 B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1612 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= 0.206 Angle : 0.555 8.109 9704 Z= 0.298 Chirality : 0.043 0.173 1118 Planarity : 0.005 0.063 1211 Dihedral : 5.928 33.604 969 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.45 % 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: -0.12 (0.28), residues: 872 helix: 0.29 (0.25), residues: 406 sheet: 0.64 (0.37), residues: 176 loop : -0.91 (0.35), residues: 290 *********************** 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 103 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.785 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 100 average time/residue: 0.2094 time to fit residues: 28.1841 Evaluate side-chains 79 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0741 time to fit residues: 1.9877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 7159 Z= 0.411 Angle : 0.610 7.761 9704 Z= 0.324 Chirality : 0.046 0.182 1118 Planarity : 0.005 0.065 1211 Dihedral : 5.408 31.159 969 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 2.25 % 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: -0.04 (0.28), residues: 872 helix: 0.67 (0.26), residues: 397 sheet: 0.09 (0.37), residues: 170 loop : -0.90 (0.34), residues: 305 *********************** 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 92 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.838 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 86 average time/residue: 0.2023 time to fit residues: 23.5998 Evaluate side-chains 73 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0705 time to fit residues: 2.1594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.0070 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2337 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 : 0.490 6.768 9704 Z= 0.261 Chirality : 0.041 0.167 1118 Planarity : 0.004 0.054 1211 Dihedral : 4.779 29.681 969 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.19 % 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: 0.25 (0.28), residues: 872 helix: 1.06 (0.27), residues: 399 sheet: 0.07 (0.36), residues: 169 loop : -0.88 (0.34), residues: 304 *********************** 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 78 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.716 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 76 average time/residue: 0.1884 time to fit residues: 19.5447 Evaluate side-chains 67 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0812 time to fit residues: 1.3974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.0970 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 overall best weight: 1.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 7159 Z= 0.294 Angle : 0.542 8.225 9704 Z= 0.285 Chirality : 0.043 0.165 1118 Planarity : 0.004 0.055 1211 Dihedral : 4.757 30.682 969 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.19 % 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: 0.11 (0.28), residues: 872 helix: 0.99 (0.27), residues: 404 sheet: -0.13 (0.37), residues: 165 loop : -0.97 (0.34), residues: 303 *********************** 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 81 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.723 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 78 average time/residue: 0.2002 time to fit residues: 21.1886 Evaluate side-chains 74 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0634 time to fit residues: 1.6901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2583 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= 0.178 Angle : 0.490 7.054 9704 Z= 0.258 Chirality : 0.041 0.157 1118 Planarity : 0.004 0.049 1211 Dihedral : 4.541 29.707 969 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.40 % 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: 0.28 (0.28), residues: 872 helix: 1.19 (0.27), residues: 402 sheet: -0.21 (0.37), residues: 170 loop : -0.85 (0.35), residues: 300 *********************** 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 71 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.852 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.2044 time to fit residues: 19.4624 Evaluate side-chains 64 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0857 time to fit residues: 1.1989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7159 Z= 0.212 Angle : 0.510 6.789 9704 Z= 0.267 Chirality : 0.042 0.187 1118 Planarity : 0.004 0.049 1211 Dihedral : 4.642 32.208 969 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.19 % 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: 0.30 (0.29), residues: 872 helix: 1.18 (0.27), residues: 408 sheet: -0.19 (0.37), residues: 170 loop : -0.86 (0.35), residues: 294 *********************** 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 75 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.831 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 73 average time/residue: 0.2101 time to fit residues: 20.8279 Evaluate side-chains 68 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0680 time to fit residues: 1.6082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 65 optimal weight: 0.0070 chunk 76 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.0000 chunk 47 optimal weight: 3.9990 overall best weight: 0.6604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2763 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= 0.172 Angle : 0.483 6.414 9704 Z= 0.253 Chirality : 0.041 0.141 1118 Planarity : 0.004 0.047 1211 Dihedral : 4.456 31.517 969 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.40 % 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: 0.47 (0.29), residues: 872 helix: 1.30 (0.27), residues: 409 sheet: -0.11 (0.37), residues: 176 loop : -0.75 (0.36), residues: 287 *********************** 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 79 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.846 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 78 average time/residue: 0.2005 time to fit residues: 21.5702 Evaluate side-chains 69 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0876 time to fit residues: 1.2394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7159 Z= 0.226 Angle : 0.516 7.091 9704 Z= 0.270 Chirality : 0.042 0.141 1118 Planarity : 0.004 0.048 1211 Dihedral : 4.554 33.679 969 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.29), residues: 872 helix: 1.30 (0.27), residues: 408 sheet: -0.21 (0.36), residues: 178 loop : -0.83 (0.36), residues: 286 *********************** 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 74 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.840 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.2019 time to fit residues: 20.4260 Evaluate side-chains 68 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0715 time to fit residues: 1.4054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2859 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= 0.205 Angle : 0.509 7.098 9704 Z= 0.266 Chirality : 0.042 0.137 1118 Planarity : 0.004 0.047 1211 Dihedral : 4.521 33.595 969 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.13 % 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: 0.44 (0.29), residues: 872 helix: 1.35 (0.27), residues: 408 sheet: -0.23 (0.36), residues: 178 loop : -0.81 (0.36), residues: 286 ********************** 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 71 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.830 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.1978 time to fit residues: 19.4730 Evaluate side-chains 69 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0665 time to fit residues: 1.2537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 28 optimal weight: 0.0020 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.167248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134404 restraints weight = 7565.289| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.57 r_work: 0.3356 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7159 Z= 0.165 Angle : 0.497 7.948 9704 Z= 0.261 Chirality : 0.041 0.180 1118 Planarity : 0.004 0.046 1211 Dihedral : 4.477 34.224 969 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.00 % 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: 0.57 (0.29), residues: 872 helix: 1.47 (0.27), residues: 408 sheet: -0.13 (0.36), residues: 176 loop : -0.80 (0.35), residues: 288 =============================================================================== Job complete usr+sys time: 1739.81 seconds wall clock time: 32 minutes 27.84 seconds (1947.84 seconds total)