Starting phenix.real_space_refine (version: dev) on Wed Feb 22 13:27:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/02_2023/7wkd_32565_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/02_2023/7wkd_32565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/02_2023/7wkd_32565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/02_2023/7wkd_32565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/02_2023/7wkd_32565_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/02_2023/7wkd_32565_trim_updated.pdb" } resolution = 3.01 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= 0.002 sd= 0.033 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 ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 250": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 328": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 17515 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3794 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5103 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3479 Classifications: {'peptide': 230} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 827 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4279 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 8.51, per 1000 atoms: 0.49 Number of scatterers: 17515 At special positions: 0 Unit cell: (121.68, 89.44, 123.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 O 1626 8.00 N 1504 7.00 C 5610 6.00 H 8712 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.03 Conformation dependent library (CDL) restraints added in 1.7 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 33.6% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.782A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 299 through 317 Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.584A pdb=" N ASP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 29 through 42 Processing helix chain 'R' and resid 27 through 51 Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.580A pdb=" N MET R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 94 through 128 removed outlier: 3.593A pdb=" N SER R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 136 removed outlier: 3.669A pdb=" N PHE R 135 " --> pdb=" O ILE R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 161 removed outlier: 4.384A pdb=" N LEU R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP R 160 " --> pdb=" O TYR R 156 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE R 161 " --> pdb=" O CYS R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 197 Proline residue: R 190 - end of helix removed outlier: 3.776A pdb=" N LEU R 193 " --> pdb=" O PRO R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 219 Processing helix chain 'R' and resid 264 through 290 Proline residue: R 281 - end of helix removed outlier: 3.672A pdb=" N VAL R 287 " --> pdb=" O ARG R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 319 Proline residue: R 317 - end of helix Processing helix chain 'R' and resid 325 through 334 Processing sheet with id= A, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.811A pdb=" N TYR A 327 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 34 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.463A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.879A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.007A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 225 through 227 removed outlier: 3.942A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 205 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 196 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 207 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 255 through 259 Processing sheet with id= G, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.282A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 51 through 55 removed outlier: 6.897A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 2 through 6 Processing sheet with id= J, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.453A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA E 39 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU E 44 " --> pdb=" O ALA E 39 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.441A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 398 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.51 Time building geometry restraints manager: 16.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8674 1.03 - 1.23: 43 1.23 - 1.42: 3814 1.42 - 1.62: 5072 1.62 - 1.81: 94 Bond restraints: 17697 Sorted by residual: bond pdb=" CA PCA C 1 " pdb=" CB PCA C 1 " ideal model delta sigma weight residual 1.530 1.224 0.306 2.00e-02 2.50e+03 2.33e+02 bond pdb=" N LPD C 3 " pdb=" CA LPD C 3 " ideal model delta sigma weight residual 1.466 1.686 -0.220 1.50e-02 4.44e+03 2.15e+02 bond pdb=" CG PCA C 1 " pdb=" CD PCA C 1 " ideal model delta sigma weight residual 1.517 1.282 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C PCA C 1 " pdb=" N HIS C 2 " ideal model delta sigma weight residual 1.329 1.486 -0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" N LPD C 3 " pdb=" CD LPD C 3 " ideal model delta sigma weight residual 1.473 1.322 0.151 1.40e-02 5.10e+03 1.17e+02 ... (remaining 17692 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.37: 459 107.37 - 114.02: 20821 114.02 - 120.68: 6047 120.68 - 127.33: 4406 127.33 - 133.98: 89 Bond angle restraints: 31822 Sorted by residual: angle pdb=" CB HIS C 2 " pdb=" CG HIS C 2 " pdb=" CD2 HIS C 2 " ideal model delta sigma weight residual 131.20 126.08 5.12 1.30e+00 5.92e-01 1.55e+01 angle pdb=" N PCA C 1 " pdb=" CA PCA C 1 " pdb=" CB PCA C 1 " ideal model delta sigma weight residual 110.50 104.42 6.08 1.70e+00 3.46e-01 1.28e+01 angle pdb=" CA PCA C 1 " pdb=" N PCA C 1 " pdb=" CD PCA C 1 " ideal model delta sigma weight residual 114.17 105.29 8.88 3.00e+00 1.11e-01 8.76e+00 angle pdb=" N LPD C 3 " pdb=" CA LPD C 3 " pdb=" CB LPD C 3 " ideal model delta sigma weight residual 103.00 106.04 -3.04 1.10e+00 8.26e-01 7.62e+00 angle pdb=" CA HIS C 2 " pdb=" C HIS C 2 " pdb=" N LPD C 3 " ideal model delta sigma weight residual 116.20 121.15 -4.95 2.00e+00 2.50e-01 6.12e+00 ... (remaining 31817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 6914 16.31 - 32.61: 206 32.61 - 48.92: 28 48.92 - 65.23: 16 65.23 - 81.53: 6 Dihedral angle restraints: 7170 sinusoidal: 3280 harmonic: 3890 Sorted by residual: dihedral pdb=" N PCA C 1 " pdb=" C PCA C 1 " pdb=" CA PCA C 1 " pdb=" CB PCA C 1 " ideal model delta harmonic sigma weight residual 122.80 114.78 8.02 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" N PHE B 239 " pdb=" CA PHE B 239 " pdb=" CB PHE B 239 " pdb=" CG PHE B 239 " ideal model delta sinusoidal sigma weight residual -180.00 -120.43 -59.57 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG B 319 " pdb=" CB ARG B 319 " pdb=" CG ARG B 319 " pdb=" CD ARG B 319 " ideal model delta sinusoidal sigma weight residual -180.00 -123.24 -56.76 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 912 0.028 - 0.055: 302 0.055 - 0.083: 87 0.083 - 0.110: 50 0.110 - 0.138: 30 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA HIS C 2 " pdb=" N HIS C 2 " pdb=" C HIS C 2 " pdb=" CB HIS C 2 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 86 " pdb=" N ILE B 86 " pdb=" C ILE B 86 " pdb=" CB ILE B 86 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL E 199 " pdb=" N VAL E 199 " pdb=" C VAL E 199 " pdb=" CB VAL E 199 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1378 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " -0.015 5.00e-02 4.00e+02 2.20e-02 7.77e-01 pdb=" N PRO E 74 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.014 5.00e-02 4.00e+02 2.06e-02 6.77e-01 pdb=" N PRO B 241 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 98 " -0.013 5.00e-02 4.00e+02 1.92e-02 5.92e-01 pdb=" N PRO B 99 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.011 5.00e-02 4.00e+02 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1507 2.23 - 2.83: 40176 2.83 - 3.42: 46692 3.42 - 4.01: 63997 4.01 - 4.60: 98500 Nonbonded interactions: 250872 Sorted by model distance: nonbonded pdb=" O THR G 5 " pdb=" H ALA G 9 " model vdw 1.643 1.850 nonbonded pdb=" HE2 HIS B 316 " pdb=" OG1 THR B 334 " model vdw 1.654 1.850 nonbonded pdb=" O LEU B 257 " pdb=" H LEU B 266 " model vdw 1.654 1.850 nonbonded pdb="HD22 ASN E 169 " pdb=" OH TYR E 173 " model vdw 1.665 1.850 nonbonded pdb=" H ARG E 86 " pdb=" OD2 ASP E 89 " model vdw 1.669 1.850 ... (remaining 250867 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: 5 Type Number sf(0) Gaussians S 63 5.16 5 C 5610 2.51 5 N 1504 2.21 5 O 1626 1.98 5 H 8712 0.53 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: 0.380 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: 0.480 Extract box with map and model: 3.230 Check model and map are aligned: 0.290 Process input model: 59.560 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 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 : 0.007 0.306 8985 Z= 0.513 Angle : 0.408 8.882 12171 Z= 0.235 Chirality : 0.037 0.138 1381 Planarity : 0.002 0.022 1536 Dihedral : 7.824 81.535 3230 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.10 % 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: -1.70 (0.23), residues: 1097 helix: 0.04 (0.25), residues: 385 sheet: -1.34 (0.30), residues: 251 loop : -1.95 (0.26), residues: 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 342 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 344 average time/residue: 0.4943 time to fit residues: 227.5066 Evaluate side-chains 299 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 245 ASN A 324 HIS B 300 ASN E 142 GLN R 43 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8985 Z= 0.279 Angle : 0.546 5.991 12171 Z= 0.285 Chirality : 0.041 0.332 1381 Planarity : 0.004 0.058 1536 Dihedral : 3.428 23.277 1225 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 2.92 % 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: -0.48 (0.25), residues: 1097 helix: 1.14 (0.27), residues: 387 sheet: -1.03 (0.30), residues: 268 loop : -1.07 (0.29), residues: 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 352 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 324 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 336 average time/residue: 0.5236 time to fit residues: 233.1299 Evaluate side-chains 322 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 300 time to evaluate : 1.386 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.1975 time to fit residues: 9.6276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 93 ASN E 142 GLN E 194 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 8985 Z= 0.376 Angle : 0.573 5.991 12171 Z= 0.307 Chirality : 0.042 0.227 1381 Planarity : 0.004 0.052 1536 Dihedral : 4.043 17.921 1225 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 2.50 % 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 (0.25), residues: 1097 helix: 1.11 (0.27), residues: 381 sheet: -0.84 (0.29), residues: 277 loop : -0.81 (0.30), residues: 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 312 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 321 average time/residue: 0.5568 time to fit residues: 234.3427 Evaluate side-chains 302 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 288 time to evaluate : 1.468 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2755 time to fit residues: 8.1487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 GLN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 8985 Z= 0.357 Angle : 0.538 5.843 12171 Z= 0.287 Chirality : 0.040 0.212 1381 Planarity : 0.004 0.042 1536 Dihedral : 4.133 17.813 1225 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 2.40 % 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: -0.05 (0.26), residues: 1097 helix: 1.27 (0.27), residues: 383 sheet: -0.65 (0.30), residues: 275 loop : -0.67 (0.30), residues: 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 308 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 314 average time/residue: 0.5520 time to fit residues: 227.4185 Evaluate side-chains 310 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 295 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2179 time to fit residues: 7.6224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 8985 Z= 0.307 Angle : 0.522 6.247 12171 Z= 0.277 Chirality : 0.040 0.203 1381 Planarity : 0.004 0.033 1536 Dihedral : 4.063 17.915 1225 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 1.56 % 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: 0.06 (0.26), residues: 1097 helix: 1.28 (0.27), residues: 386 sheet: -0.60 (0.30), residues: 263 loop : -0.55 (0.31), residues: 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 327 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 312 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 315 average time/residue: 0.5565 time to fit residues: 230.3498 Evaluate side-chains 312 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 301 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2088 time to fit residues: 5.9575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 GLN G 58 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 8985 Z= 0.450 Angle : 0.580 5.888 12171 Z= 0.313 Chirality : 0.043 0.216 1381 Planarity : 0.004 0.039 1536 Dihedral : 4.445 19.680 1225 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 1.88 % 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: -0.14 (0.25), residues: 1097 helix: 0.94 (0.26), residues: 393 sheet: -0.47 (0.31), residues: 253 loop : -0.68 (0.30), residues: 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 329 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 311 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 315 average time/residue: 0.5323 time to fit residues: 221.8620 Evaluate side-chains 307 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 292 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2076 time to fit residues: 7.2090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8985 Z= 0.213 Angle : 0.512 5.688 12171 Z= 0.270 Chirality : 0.040 0.183 1381 Planarity : 0.004 0.058 1536 Dihedral : 4.087 18.966 1225 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.73 % 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 (0.26), residues: 1097 helix: 1.24 (0.27), residues: 393 sheet: -0.27 (0.31), residues: 237 loop : -0.49 (0.30), residues: 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 302 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 305 average time/residue: 0.5274 time to fit residues: 213.4677 Evaluate side-chains 303 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 297 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1920 time to fit residues: 3.8730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8985 Z= 0.236 Angle : 0.509 5.604 12171 Z= 0.270 Chirality : 0.040 0.188 1381 Planarity : 0.004 0.051 1536 Dihedral : 4.067 19.202 1225 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1097 helix: 1.40 (0.27), residues: 393 sheet: -0.26 (0.31), residues: 237 loop : -0.47 (0.30), residues: 467 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 304 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 299 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 299 average time/residue: 0.5747 time to fit residues: 226.7545 Evaluate side-chains 294 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 289 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2336 time to fit residues: 3.8204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8985 Z= 0.230 Angle : 0.510 5.912 12171 Z= 0.271 Chirality : 0.040 0.203 1381 Planarity : 0.004 0.038 1536 Dihedral : 4.044 19.371 1225 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.21 % 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: 0.38 (0.26), residues: 1097 helix: 1.49 (0.27), residues: 388 sheet: -0.27 (0.31), residues: 237 loop : -0.42 (0.30), residues: 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 297 average time/residue: 0.5659 time to fit residues: 220.7418 Evaluate side-chains 292 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1995 time to fit residues: 2.2460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8985 Z= 0.262 Angle : 0.520 6.217 12171 Z= 0.276 Chirality : 0.040 0.192 1381 Planarity : 0.004 0.042 1536 Dihedral : 4.103 20.468 1225 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.31 % 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 (0.26), residues: 1097 helix: 1.49 (0.27), residues: 391 sheet: -0.35 (0.31), residues: 253 loop : -0.41 (0.31), residues: 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 290 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 290 average time/residue: 0.5608 time to fit residues: 212.5155 Evaluate side-chains 287 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 284 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2104 time to fit residues: 2.9203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 76 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116185 restraints weight = 36239.067| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.83 r_work: 0.3464 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.6810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 8985 Z= 0.312 Angle : 0.537 6.039 12171 Z= 0.287 Chirality : 0.041 0.197 1381 Planarity : 0.004 0.039 1536 Dihedral : 4.218 22.197 1225 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.31 % 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 (0.26), residues: 1097 helix: 1.43 (0.27), residues: 385 sheet: -0.39 (0.31), residues: 253 loop : -0.45 (0.30), residues: 459 =============================================================================== Job complete usr+sys time: 5610.45 seconds wall clock time: 99 minutes 26.89 seconds (5966.89 seconds total)