Starting phenix.real_space_refine on Sun Mar 17 10:36:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/03_2024/7wkd_32565_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/03_2024/7wkd_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_32565/03_2024/7wkd_32565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/03_2024/7wkd_32565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/03_2024/7wkd_32565_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wkd_32565/03_2024/7wkd_32565_trim_updated.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 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. 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-5265/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: 7.94, per 1000 atoms: 0.45 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: 13.97 Conformation dependent library (CDL) restraints added in 1.9 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: 2.54 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: 6.41 Time building geometry restraints manager: 14.54 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: 7947 16.31 - 32.61: 267 32.61 - 48.92: 73 48.92 - 65.23: 62 65.23 - 81.53: 6 Dihedral angle restraints: 8355 sinusoidal: 4465 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 8352 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 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: 0.390 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: 0.270 Extract box with map and model: 2.860 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 58.870 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 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 % Allowed : 2.92 % Favored : 96.77 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.001 0.000 HIS A 329 PHE 0.007 0.001 PHE A 189 TYR 0.004 0.000 TYR E 228 ARG 0.001 0.000 ARG R 57 *********************** 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 : 1.375 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 REVERT: A 193 LYS cc_start: 0.7974 (tptt) cc_final: 0.7769 (tptt) REVERT: A 276 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6779 (tm-30) REVERT: B 35 LEU cc_start: 0.6859 (tp) cc_final: 0.6623 (tt) REVERT: B 133 THR cc_start: 0.8063 (p) cc_final: 0.7725 (t) REVERT: B 203 LEU cc_start: 0.7683 (mt) cc_final: 0.7442 (mp) REVERT: B 239 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7244 (t80) REVERT: B 244 ASN cc_start: 0.7569 (m-40) cc_final: 0.7338 (m110) REVERT: B 251 ASP cc_start: 0.5791 (p0) cc_final: 0.5280 (p0) REVERT: B 252 ASP cc_start: 0.5060 (t0) cc_final: 0.4729 (t0) REVERT: E 167 HIS cc_start: 0.7542 (t70) cc_final: 0.7303 (t-90) REVERT: E 184 SER cc_start: 0.7816 (p) cc_final: 0.7579 (t) REVERT: G 47 ASP cc_start: 0.7390 (t0) cc_final: 0.7089 (t0) REVERT: R 131 ILE cc_start: 0.7288 (mm) cc_final: 0.7067 (mm) REVERT: R 263 GLN cc_start: 0.5626 (pm20) cc_final: 0.4815 (pm20) REVERT: R 319 ILE cc_start: 0.7599 (tp) cc_final: 0.7217 (pt) outliers start: 3 outliers final: 0 residues processed: 344 average time/residue: 0.4915 time to fit residues: 228.1821 Evaluate side-chains 300 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 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: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 324 HIS B 300 ASN E 142 GLN ** R 43 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8985 Z= 0.224 Angle : 0.480 5.573 12171 Z= 0.250 Chirality : 0.039 0.226 1381 Planarity : 0.004 0.051 1536 Dihedral : 3.467 58.027 1227 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.50 % Allowed : 10.22 % Favored : 87.28 % 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 (0.25), residues: 1097 helix: 1.25 (0.27), residues: 381 sheet: -1.00 (0.30), residues: 256 loop : -1.13 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 248 HIS 0.010 0.001 HIS A 324 PHE 0.017 0.002 PHE B 240 TYR 0.012 0.001 TYR A 306 ARG 0.007 0.001 ARG B 224 *********************** 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 350 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 326 time to evaluate : 1.437 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: A 46 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7995 (ptpt) REVERT: A 241 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7861 (ttpt) REVERT: A 309 ARG cc_start: 0.6115 (ttp-170) cc_final: 0.5437 (ttp-170) REVERT: A 348 ASP cc_start: 0.7204 (t0) cc_final: 0.6841 (t0) REVERT: B 35 LEU cc_start: 0.6903 (tp) cc_final: 0.6696 (tt) REVERT: B 88 ASP cc_start: 0.7440 (t0) cc_final: 0.7095 (t0) REVERT: B 123 ASP cc_start: 0.7145 (t0) cc_final: 0.6624 (t0) REVERT: B 133 THR cc_start: 0.8276 (p) cc_final: 0.7916 (t) REVERT: B 194 SER cc_start: 0.7926 (p) cc_final: 0.7696 (t) REVERT: B 195 LEU cc_start: 0.7320 (mt) cc_final: 0.7089 (mt) REVERT: B 203 LEU cc_start: 0.7944 (mt) cc_final: 0.7707 (mp) REVERT: B 239 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.6843 (t80) REVERT: B 244 ASN cc_start: 0.7603 (m-40) cc_final: 0.7351 (m110) REVERT: B 254 THR cc_start: 0.7832 (p) cc_final: 0.6685 (m) REVERT: B 345 ASN cc_start: 0.5965 (t0) cc_final: 0.5755 (t0) REVERT: E 167 HIS cc_start: 0.7837 (t70) cc_final: 0.7468 (t-90) REVERT: G 47 ASP cc_start: 0.7638 (t0) cc_final: 0.7421 (t0) REVERT: R 143 LYS cc_start: 0.7778 (mtpp) cc_final: 0.7387 (ttmm) REVERT: R 263 GLN cc_start: 0.5857 (pm20) cc_final: 0.5123 (pm20) outliers start: 24 outliers final: 18 residues processed: 334 average time/residue: 0.5159 time to fit residues: 229.6945 Evaluate side-chains 323 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 304 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 280 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 216 ASN A 344 ASN A 359 ASN B 93 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 ASN C 2 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8985 Z= 0.339 Angle : 0.541 5.686 12171 Z= 0.290 Chirality : 0.041 0.205 1381 Planarity : 0.004 0.050 1536 Dihedral : 4.164 59.113 1227 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.17 % Allowed : 12.51 % Favored : 83.32 % 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: -0.10 (0.26), residues: 1097 helix: 1.40 (0.27), residues: 380 sheet: -0.87 (0.30), residues: 269 loop : -0.73 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 160 HIS 0.007 0.002 HIS A 197 PHE 0.020 0.002 PHE B 240 TYR 0.022 0.002 TYR B 116 ARG 0.013 0.001 ARG B 288 *********************** 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 343 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 303 time to evaluate : 1.520 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: A 31 ARG cc_start: 0.7168 (mtm110) cc_final: 0.6943 (mtm110) REVERT: A 298 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.7060 (t70) REVERT: A 348 ASP cc_start: 0.7268 (t0) cc_final: 0.6950 (t0) REVERT: B 53 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7780 (mmt180) REVERT: B 123 ASP cc_start: 0.7266 (t0) cc_final: 0.6684 (t0) REVERT: B 129 TYR cc_start: 0.8165 (m-80) cc_final: 0.7361 (m-80) REVERT: B 194 SER cc_start: 0.7815 (p) cc_final: 0.7494 (t) REVERT: B 205 VAL cc_start: 0.8347 (p) cc_final: 0.8145 (m) REVERT: B 244 ASN cc_start: 0.7775 (m-40) cc_final: 0.7563 (m-40) REVERT: B 259 ASP cc_start: 0.6762 (t70) cc_final: 0.6491 (t0) REVERT: B 273 ASN cc_start: 0.7255 (m110) cc_final: 0.6837 (m110) REVERT: B 321 SER cc_start: 0.7693 (t) cc_final: 0.7342 (p) REVERT: B 322 CYS cc_start: 0.7399 (p) cc_final: 0.7058 (p) REVERT: B 345 ASN cc_start: 0.6163 (t0) cc_final: 0.5938 (t0) REVERT: E 167 HIS cc_start: 0.8003 (t70) cc_final: 0.7635 (t-90) REVERT: E 220 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7106 (mm-30) REVERT: R 298 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6654 (mm-30) outliers start: 40 outliers final: 27 residues processed: 319 average time/residue: 0.5250 time to fit residues: 222.1264 Evaluate side-chains 321 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 293 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.4929 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= 0.212 Angle : 0.481 5.515 12171 Z= 0.251 Chirality : 0.038 0.194 1381 Planarity : 0.004 0.039 1536 Dihedral : 4.052 59.829 1227 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.13 % Allowed : 15.54 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1097 helix: 1.76 (0.28), residues: 383 sheet: -0.55 (0.30), residues: 264 loop : -0.51 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.007 0.001 HIS E 232 PHE 0.019 0.001 PHE B 204 TYR 0.014 0.001 TYR B 116 ARG 0.002 0.000 ARG B 288 *********************** 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 328 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 298 time to evaluate : 1.352 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: A 32 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7094 (mtm-85) REVERT: A 298 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.7028 (t70) REVERT: A 338 ASN cc_start: 0.7990 (t0) cc_final: 0.7761 (t0) REVERT: A 348 ASP cc_start: 0.7229 (t0) cc_final: 0.6922 (t0) REVERT: B 53 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7805 (mmt180) REVERT: B 73 ARG cc_start: 0.7484 (ttt180) cc_final: 0.7282 (mtp180) REVERT: B 123 ASP cc_start: 0.7286 (t0) cc_final: 0.6667 (t0) REVERT: B 129 TYR cc_start: 0.8074 (m-80) cc_final: 0.7228 (m-80) REVERT: B 205 VAL cc_start: 0.8369 (p) cc_final: 0.8149 (m) REVERT: B 244 ASN cc_start: 0.7755 (m-40) cc_final: 0.7551 (m110) REVERT: B 259 ASP cc_start: 0.6755 (t70) cc_final: 0.6487 (t0) REVERT: B 273 ASN cc_start: 0.7268 (m110) cc_final: 0.6862 (m110) REVERT: B 321 SER cc_start: 0.7569 (t) cc_final: 0.7237 (p) REVERT: B 322 CYS cc_start: 0.7291 (p) cc_final: 0.6967 (p) REVERT: E 220 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7172 (mm-30) outliers start: 30 outliers final: 24 residues processed: 309 average time/residue: 0.5663 time to fit residues: 230.4744 Evaluate side-chains 320 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 295 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 82 ASN Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.0010 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8985 Z= 0.406 Angle : 0.540 4.738 12171 Z= 0.290 Chirality : 0.041 0.224 1381 Planarity : 0.004 0.049 1536 Dihedral : 4.469 59.153 1227 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.34 % Allowed : 17.31 % Favored : 79.35 % 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: 0.18 (0.26), residues: 1097 helix: 1.38 (0.27), residues: 388 sheet: -0.45 (0.30), residues: 275 loop : -0.54 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 160 HIS 0.010 0.002 HIS E 232 PHE 0.023 0.002 PHE B 240 TYR 0.018 0.002 TYR E 190 ARG 0.002 0.000 ARG A 15 *********************** 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 339 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 307 time to evaluate : 1.408 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: A 233 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7089 (mp) REVERT: B 53 ARG cc_start: 0.8096 (mmt180) cc_final: 0.7875 (mmt180) REVERT: B 102 SER cc_start: 0.8134 (t) cc_final: 0.7669 (p) REVERT: B 123 ASP cc_start: 0.7253 (t0) cc_final: 0.6648 (t0) REVERT: B 129 TYR cc_start: 0.8329 (m-80) cc_final: 0.7841 (m-80) REVERT: B 175 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7084 (t0) REVERT: B 178 THR cc_start: 0.8213 (m) cc_final: 0.7980 (p) REVERT: B 205 VAL cc_start: 0.8364 (p) cc_final: 0.8156 (m) REVERT: B 244 ASN cc_start: 0.7767 (m-40) cc_final: 0.7566 (m-40) REVERT: B 259 ASP cc_start: 0.6802 (t70) cc_final: 0.6565 (t0) REVERT: B 303 ASP cc_start: 0.7491 (t70) cc_final: 0.7095 (t0) REVERT: B 321 SER cc_start: 0.7661 (t) cc_final: 0.7312 (p) REVERT: B 322 CYS cc_start: 0.7363 (p) cc_final: 0.7069 (p) REVERT: E 220 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7247 (mm-30) REVERT: R 318 VAL cc_start: 0.8100 (t) cc_final: 0.7889 (p) outliers start: 32 outliers final: 27 residues processed: 319 average time/residue: 0.5472 time to fit residues: 231.6596 Evaluate side-chains 327 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 298 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8985 Z= 0.210 Angle : 0.486 5.249 12171 Z= 0.255 Chirality : 0.039 0.191 1381 Planarity : 0.003 0.044 1536 Dihedral : 4.212 58.141 1227 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.23 % Allowed : 18.77 % Favored : 78.00 % 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: 0.47 (0.26), residues: 1097 helix: 1.74 (0.27), residues: 382 sheet: -0.42 (0.31), residues: 256 loop : -0.38 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.012 0.001 HIS A 329 PHE 0.015 0.001 PHE B 204 TYR 0.013 0.001 TYR B 116 ARG 0.002 0.000 ARG A 54 *********************** 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 334 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 303 time to evaluate : 1.461 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: A 233 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7077 (mp) REVERT: A 342 ILE cc_start: 0.8040 (mm) cc_final: 0.7782 (mt) REVERT: B 53 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7853 (mmt180) REVERT: B 102 SER cc_start: 0.8123 (t) cc_final: 0.7677 (p) REVERT: B 123 ASP cc_start: 0.7242 (t0) cc_final: 0.6616 (t0) REVERT: B 129 TYR cc_start: 0.8209 (m-80) cc_final: 0.7635 (m-80) REVERT: B 175 ASP cc_start: 0.7310 (t0) cc_final: 0.7029 (t0) REVERT: B 244 ASN cc_start: 0.7766 (m-40) cc_final: 0.7547 (m-40) REVERT: B 259 ASP cc_start: 0.6749 (t70) cc_final: 0.6519 (t0) REVERT: B 321 SER cc_start: 0.7597 (t) cc_final: 0.7246 (p) REVERT: B 322 CYS cc_start: 0.7294 (p) cc_final: 0.6988 (p) REVERT: E 167 HIS cc_start: 0.7987 (t70) cc_final: 0.7605 (t-90) REVERT: R 318 VAL cc_start: 0.8105 (t) cc_final: 0.7897 (p) outliers start: 31 outliers final: 26 residues processed: 315 average time/residue: 0.5803 time to fit residues: 241.3851 Evaluate side-chains 325 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 298 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** G 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8985 Z= 0.183 Angle : 0.478 5.285 12171 Z= 0.249 Chirality : 0.039 0.191 1381 Planarity : 0.003 0.049 1536 Dihedral : 4.121 57.744 1227 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.02 % Allowed : 19.08 % Favored : 77.89 % 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: 0.61 (0.26), residues: 1097 helix: 1.89 (0.27), residues: 382 sheet: -0.40 (0.31), residues: 256 loop : -0.29 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.007 0.001 HIS A 329 PHE 0.013 0.001 PHE B 204 TYR 0.011 0.001 TYR B 64 ARG 0.001 0.000 ARG E 17 *********************** 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 328 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 299 time to evaluate : 1.469 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: A 233 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7068 (mp) REVERT: A 276 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 298 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.7043 (t70) REVERT: A 342 ILE cc_start: 0.8049 (mm) cc_final: 0.7810 (mt) REVERT: B 53 ARG cc_start: 0.8070 (mmt180) cc_final: 0.7862 (mmt180) REVERT: B 102 SER cc_start: 0.8125 (t) cc_final: 0.7697 (p) REVERT: B 123 ASP cc_start: 0.7235 (t0) cc_final: 0.6612 (t0) REVERT: B 129 TYR cc_start: 0.8198 (m-80) cc_final: 0.7592 (m-80) REVERT: B 134 ARG cc_start: 0.7562 (mmm160) cc_final: 0.7220 (mmm-85) REVERT: B 175 ASP cc_start: 0.7286 (t0) cc_final: 0.7041 (t0) REVERT: B 244 ASN cc_start: 0.7709 (m-40) cc_final: 0.7475 (m110) REVERT: B 259 ASP cc_start: 0.6736 (t70) cc_final: 0.6501 (t0) REVERT: B 321 SER cc_start: 0.7535 (t) cc_final: 0.7216 (p) REVERT: B 322 CYS cc_start: 0.7275 (p) cc_final: 0.6945 (p) REVERT: E 167 HIS cc_start: 0.7980 (t70) cc_final: 0.7578 (t-90) outliers start: 29 outliers final: 25 residues processed: 309 average time/residue: 0.5352 time to fit residues: 219.0076 Evaluate side-chains 325 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 298 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 321 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 ASN R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8985 Z= 0.359 Angle : 0.542 6.517 12171 Z= 0.289 Chirality : 0.041 0.214 1381 Planarity : 0.004 0.052 1536 Dihedral : 4.461 57.289 1227 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.55 % Allowed : 18.98 % Favored : 77.48 % 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: 0.39 (0.26), residues: 1097 helix: 1.57 (0.27), residues: 381 sheet: -0.39 (0.30), residues: 260 loop : -0.36 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 160 HIS 0.005 0.001 HIS E 232 PHE 0.020 0.002 PHE B 240 TYR 0.015 0.002 TYR E 190 ARG 0.003 0.000 ARG A 300 *********************** 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 334 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 300 time to evaluate : 1.412 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: A 185 PHE cc_start: 0.7134 (t80) cc_final: 0.6828 (t80) REVERT: A 186 GLU cc_start: 0.6455 (tm-30) cc_final: 0.5799 (tt0) REVERT: A 197 HIS cc_start: 0.7135 (m170) cc_final: 0.6848 (m170) REVERT: A 233 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7084 (mp) REVERT: A 276 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 342 ILE cc_start: 0.8088 (mm) cc_final: 0.7877 (mt) REVERT: B 102 SER cc_start: 0.8181 (t) cc_final: 0.7792 (p) REVERT: B 123 ASP cc_start: 0.7405 (t0) cc_final: 0.6765 (t0) REVERT: B 129 TYR cc_start: 0.8396 (m-80) cc_final: 0.6843 (m-80) REVERT: B 134 ARG cc_start: 0.7658 (mmm160) cc_final: 0.7312 (mmm-85) REVERT: B 244 ASN cc_start: 0.7758 (m-40) cc_final: 0.7539 (m110) REVERT: B 259 ASP cc_start: 0.6783 (t70) cc_final: 0.6545 (t0) REVERT: B 321 SER cc_start: 0.7609 (t) cc_final: 0.7197 (p) REVERT: B 322 CYS cc_start: 0.7337 (p) cc_final: 0.7071 (p) REVERT: E 86 ARG cc_start: 0.8085 (ptp-170) cc_final: 0.7863 (mtm-85) REVERT: R 327 PHE cc_start: 0.7807 (t80) cc_final: 0.7530 (t80) outliers start: 34 outliers final: 30 residues processed: 311 average time/residue: 0.5288 time to fit residues: 216.9162 Evaluate side-chains 321 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 290 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 82 ASN Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 321 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** 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: 0.6984 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8985 Z= 0.215 Angle : 0.507 6.561 12171 Z= 0.266 Chirality : 0.040 0.190 1381 Planarity : 0.004 0.051 1536 Dihedral : 4.342 57.130 1227 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.92 % Allowed : 20.44 % Favored : 76.64 % 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: 0.56 (0.26), residues: 1097 helix: 1.71 (0.27), residues: 381 sheet: -0.31 (0.31), residues: 252 loop : -0.27 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 174 HIS 0.006 0.001 HIS A 329 PHE 0.018 0.001 PHE B 246 TYR 0.010 0.001 TYR B 64 ARG 0.003 0.000 ARG A 247 *********************** 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 328 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 300 time to evaluate : 1.373 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: A 185 PHE cc_start: 0.7131 (t80) cc_final: 0.6837 (t80) REVERT: A 197 HIS cc_start: 0.7125 (m170) cc_final: 0.6793 (m-70) REVERT: A 233 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7094 (mp) REVERT: A 248 TRP cc_start: 0.8296 (m100) cc_final: 0.7875 (m100) REVERT: A 276 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 342 ILE cc_start: 0.8082 (mm) cc_final: 0.7875 (mt) REVERT: B 53 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7905 (mmt180) REVERT: B 102 SER cc_start: 0.8155 (t) cc_final: 0.7748 (p) REVERT: B 123 ASP cc_start: 0.7379 (t0) cc_final: 0.6759 (t0) REVERT: B 129 TYR cc_start: 0.8351 (m-80) cc_final: 0.6692 (m-80) REVERT: B 259 ASP cc_start: 0.6725 (t70) cc_final: 0.6513 (t0) REVERT: B 321 SER cc_start: 0.7578 (t) cc_final: 0.7204 (p) REVERT: B 322 CYS cc_start: 0.7304 (p) cc_final: 0.7022 (p) REVERT: E 86 ARG cc_start: 0.8079 (ptp-170) cc_final: 0.7859 (mtm-85) REVERT: E 167 HIS cc_start: 0.8055 (t70) cc_final: 0.7700 (t-90) REVERT: G 26 ARG cc_start: 0.7561 (mtt-85) cc_final: 0.7187 (mtt-85) REVERT: G 45 LYS cc_start: 0.8426 (mttm) cc_final: 0.8194 (mttm) REVERT: R 327 PHE cc_start: 0.7804 (t80) cc_final: 0.7532 (t80) outliers start: 28 outliers final: 26 residues processed: 309 average time/residue: 0.5401 time to fit residues: 217.6006 Evaluate side-chains 325 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 298 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN C 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8985 Z= 0.161 Angle : 0.484 5.676 12171 Z= 0.253 Chirality : 0.039 0.177 1381 Planarity : 0.003 0.051 1536 Dihedral : 4.168 56.849 1227 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.40 % Allowed : 21.79 % Favored : 75.81 % 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: 0.69 (0.26), residues: 1097 helix: 1.90 (0.27), residues: 385 sheet: -0.45 (0.31), residues: 255 loop : -0.15 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 87 HIS 0.005 0.001 HIS A 329 PHE 0.011 0.001 PHE B 246 TYR 0.010 0.001 TYR B 129 ARG 0.002 0.000 ARG B 319 ********************** 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 307 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 1.491 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: A 17 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7656 (mmtm) REVERT: A 185 PHE cc_start: 0.7145 (t80) cc_final: 0.6860 (t80) REVERT: A 197 HIS cc_start: 0.7100 (m170) cc_final: 0.6804 (m-70) REVERT: A 233 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7054 (mp) REVERT: A 248 TRP cc_start: 0.8168 (m100) cc_final: 0.7697 (m100) REVERT: A 276 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7120 (tm-30) REVERT: A 298 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6781 (t0) REVERT: A 341 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7632 (mtt90) REVERT: A 348 ASP cc_start: 0.7142 (t70) cc_final: 0.6933 (t70) REVERT: B 102 SER cc_start: 0.8144 (t) cc_final: 0.7731 (p) REVERT: B 123 ASP cc_start: 0.7230 (t0) cc_final: 0.6612 (t0) REVERT: B 129 TYR cc_start: 0.8227 (m-80) cc_final: 0.7717 (m-80) REVERT: B 144 LEU cc_start: 0.7597 (pp) cc_final: 0.7397 (pp) REVERT: B 259 ASP cc_start: 0.6700 (t70) cc_final: 0.6478 (t0) REVERT: B 321 SER cc_start: 0.7497 (t) cc_final: 0.7135 (p) REVERT: B 322 CYS cc_start: 0.7196 (p) cc_final: 0.6913 (p) REVERT: E 86 ARG cc_start: 0.8059 (ptp-170) cc_final: 0.7842 (mtm-85) REVERT: E 167 HIS cc_start: 0.8017 (t70) cc_final: 0.7669 (t-90) REVERT: G 45 LYS cc_start: 0.8436 (mttm) cc_final: 0.8191 (mttm) REVERT: R 327 PHE cc_start: 0.7792 (t80) cc_final: 0.7524 (t80) outliers start: 23 outliers final: 20 residues processed: 295 average time/residue: 0.5467 time to fit residues: 212.4587 Evaluate side-chains 304 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 282 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 189 SER 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: 0.4980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 246 ASN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN C 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119173 restraints weight = 37074.918| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.83 r_work: 0.3491 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8985 Z= 0.197 Angle : 0.490 5.864 12171 Z= 0.255 Chirality : 0.039 0.184 1381 Planarity : 0.003 0.050 1536 Dihedral : 4.177 56.971 1227 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.92 % Allowed : 21.17 % Favored : 75.91 % 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: 0.73 (0.26), residues: 1097 helix: 1.99 (0.27), residues: 378 sheet: -0.35 (0.30), residues: 265 loop : -0.20 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 302 HIS 0.005 0.001 HIS C 2 PHE 0.010 0.001 PHE B 240 TYR 0.009 0.001 TYR B 129 ARG 0.002 0.000 ARG A 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5697.49 seconds wall clock time: 100 minutes 57.15 seconds (6057.15 seconds total)