Starting phenix.real_space_refine on Fri Mar 15 21:25:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n9y_3605/03_2024/5n9y_3605.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n9y_3605/03_2024/5n9y_3605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n9y_3605/03_2024/5n9y_3605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n9y_3605/03_2024/5n9y_3605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n9y_3605/03_2024/5n9y_3605.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n9y_3605/03_2024/5n9y_3605.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 8080 2.51 5 N 2290 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E ARG 323": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12835 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "C" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "D" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "E" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Time building chain proxies: 6.96, per 1000 atoms: 0.54 Number of scatterers: 12835 At special positions: 0 Unit cell: (118.69, 118.69, 127.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 2370 8.00 N 2290 7.00 C 8080 6.00 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: 5.27 Conformation dependent library (CDL) restraints added in 1.8 seconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 56.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 64 through 70 removed outlier: 4.207A pdb=" N ASP A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 69 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.927A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 167 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.602A pdb=" N ASN A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 176 " --> pdb=" O GLU A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 186 through 213 removed outlier: 3.516A pdb=" N LEU A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 4.626A pdb=" N ASP A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 267 removed outlier: 3.569A pdb=" N GLY A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 4.278A pdb=" N ALA A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.524A pdb=" N THR A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 removed outlier: 3.708A pdb=" N ILE A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL A 311 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 142 through 170 Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.871A pdb=" N LEU B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 220 through 277 removed outlier: 3.655A pdb=" N ILE B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 removed outlier: 4.021A pdb=" N THR B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 322 removed outlier: 4.171A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 311 " --> pdb=" O CYS B 307 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 59 Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 68 through 72 removed outlier: 4.117A pdb=" N GLY C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 135 removed outlier: 4.606A pdb=" N GLU C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 171 Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.825A pdb=" N ASN C 175 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 212 removed outlier: 3.568A pdb=" N LEU C 190 " --> pdb=" O PHE C 186 " (cutoff:3.500A) Proline residue: C 203 - end of helix removed outlier: 4.099A pdb=" N ASP C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 277 removed outlier: 3.664A pdb=" N ALA C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 302 through 325 Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 68 through 72 removed outlier: 4.032A pdb=" N GLY D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'D' and resid 142 through 172 Processing helix chain 'D' and resid 186 through 214 removed outlier: 3.599A pdb=" N LEU D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) Proline residue: D 203 - end of helix removed outlier: 3.840A pdb=" N ASP D 206 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 277 Processing helix chain 'D' and resid 278 through 288 removed outlier: 3.953A pdb=" N PHE D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 324 removed outlier: 4.057A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 311 " --> pdb=" O CYS D 307 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 removed outlier: 4.347A pdb=" N VAL E 9 " --> pdb=" O LYS E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 142 through 170 Processing helix chain 'E' and resid 171 through 176 removed outlier: 3.818A pdb=" N ASP E 174 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN E 175 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 213 removed outlier: 3.554A pdb=" N LEU E 190 " --> pdb=" O PHE E 186 " (cutoff:3.500A) Proline residue: E 203 - end of helix removed outlier: 4.620A pdb=" N ASP E 206 " --> pdb=" O ALA E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 276 removed outlier: 3.793A pdb=" N GLY E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 269 " --> pdb=" O ARG E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 288 removed outlier: 3.732A pdb=" N GLY E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 322 removed outlier: 4.737A pdb=" N VAL E 311 " --> pdb=" O CYS E 307 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 4.066A pdb=" N ILE A 4 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 4.029A pdb=" N LYS A 27 " --> pdb=" O MET A 19 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS A 41 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N SER A 118 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 43 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 105 " --> pdb=" O CYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.612A pdb=" N ILE B 4 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.901A pdb=" N LYS B 27 " --> pdb=" O MET B 19 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N CYS B 41 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER B 118 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 43 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ARG B 120 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 45 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 removed outlier: 4.185A pdb=" N ILE C 4 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 35 " --> pdb=" O ILE C 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 26 through 28 removed outlier: 3.931A pdb=" N ILE C 116 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 43 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 118 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 120 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 105 " --> pdb=" O CYS C 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.841A pdb=" N ILE D 4 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.592A pdb=" N PHE D 16 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N CYS D 41 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER D 118 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU D 43 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ARG D 120 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU D 45 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'E' and resid 16 through 19 Processing sheet with id=AB2, first strand: chain 'E' and resid 79 through 82 773 hydrogen bonds defined for protein. 2235 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: 3.55 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4265 1.34 - 1.46: 2240 1.46 - 1.57: 6420 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 13085 Sorted by residual: bond pdb=" CG1 ILE D 93 " pdb=" CD1 ILE D 93 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.08e+00 bond pdb=" C LEU B 61 " pdb=" N LEU B 62 " ideal model delta sigma weight residual 1.339 1.227 0.112 5.57e-02 3.22e+02 4.08e+00 bond pdb=" CB ARG C 78 " pdb=" CG ARG C 78 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.47e+00 bond pdb=" CB ASP C 239 " pdb=" CG ASP C 239 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.38e+00 bond pdb=" CB TRP B 18 " pdb=" CG TRP B 18 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.31e+00 ... (remaining 13080 not shown) Histogram of bond angle deviations from ideal: 96.68 - 104.21: 222 104.21 - 111.73: 5677 111.73 - 119.25: 5388 119.25 - 126.78: 6258 126.78 - 134.30: 215 Bond angle restraints: 17760 Sorted by residual: angle pdb=" N ARG C 76 " pdb=" CA ARG C 76 " pdb=" C ARG C 76 " ideal model delta sigma weight residual 108.13 113.89 -5.76 9.00e-01 1.23e+00 4.09e+01 angle pdb=" N ILE E 93 " pdb=" CA ILE E 93 " pdb=" C ILE E 93 " ideal model delta sigma weight residual 106.42 114.25 -7.83 1.51e+00 4.39e-01 2.69e+01 angle pdb=" C LEU A 238 " pdb=" N ASP A 239 " pdb=" CA ASP A 239 " ideal model delta sigma weight residual 121.14 112.63 8.51 1.75e+00 3.27e-01 2.36e+01 angle pdb=" N ILE D 93 " pdb=" CA ILE D 93 " pdb=" C ILE D 93 " ideal model delta sigma weight residual 106.42 113.55 -7.13 1.51e+00 4.39e-01 2.23e+01 angle pdb=" N ILE D 93 " pdb=" CA ILE D 93 " pdb=" CB ILE D 93 " ideal model delta sigma weight residual 112.65 107.98 4.67 1.00e+00 1.00e+00 2.18e+01 ... (remaining 17755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 7196 17.18 - 34.35: 533 34.35 - 51.53: 116 51.53 - 68.71: 5 68.71 - 85.89: 10 Dihedral angle restraints: 7860 sinusoidal: 3205 harmonic: 4655 Sorted by residual: dihedral pdb=" CA GLY D 95 " pdb=" C GLY D 95 " pdb=" N SER D 96 " pdb=" CA SER D 96 " ideal model delta harmonic sigma weight residual 180.00 149.28 30.72 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA MET D 111 " pdb=" C MET D 111 " pdb=" N ASP D 112 " pdb=" CA ASP D 112 " ideal model delta harmonic sigma weight residual 180.00 149.55 30.45 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA ARG B 210 " pdb=" C ARG B 210 " pdb=" N LEU B 211 " pdb=" CA LEU B 211 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1460 0.071 - 0.141: 460 0.141 - 0.212: 73 0.212 - 0.283: 9 0.283 - 0.353: 3 Chirality restraints: 2005 Sorted by residual: chirality pdb=" CB ILE C 93 " pdb=" CA ILE C 93 " pdb=" CG1 ILE C 93 " pdb=" CG2 ILE C 93 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU C 104 " pdb=" CB LEU C 104 " pdb=" CD1 LEU C 104 " pdb=" CD2 LEU C 104 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 2002 not shown) Planarity restraints: 2315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 76 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 77 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 202 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO E 203 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO E 203 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 203 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 202 " 0.052 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO B 203 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " 0.044 5.00e-02 4.00e+02 ... (remaining 2312 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2625 2.77 - 3.30: 12882 3.30 - 3.83: 22989 3.83 - 4.37: 26135 4.37 - 4.90: 41431 Nonbonded interactions: 106062 Sorted by model distance: nonbonded pdb=" O CYS C 151 " pdb=" OG1 THR C 155 " model vdw 2.233 2.440 nonbonded pdb=" O GLN A 54 " pdb=" OG1 THR A 58 " model vdw 2.244 2.440 nonbonded pdb=" O CYS B 151 " pdb=" OG1 THR B 155 " model vdw 2.249 2.440 nonbonded pdb=" O ARG D 266 " pdb=" OG1 THR D 269 " model vdw 2.263 2.440 nonbonded pdb=" O GLN C 54 " pdb=" OG1 THR C 58 " model vdw 2.267 2.440 ... (remaining 106057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.930 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 34.960 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 13085 Z= 0.507 Angle : 1.295 15.421 17760 Z= 0.674 Chirality : 0.068 0.353 2005 Planarity : 0.009 0.082 2315 Dihedral : 12.872 85.887 4860 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.02 % Allowed : 10.40 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -5.18 (0.15), residues: 1625 helix: -3.34 (0.12), residues: 890 sheet: -2.62 (0.38), residues: 165 loop : -3.52 (0.19), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 42 HIS 0.006 0.002 HIS A 166 PHE 0.028 0.004 PHE C 306 TYR 0.020 0.003 TYR E 268 ARG 0.045 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 413 time to evaluate : 1.553 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 65 ASN cc_start: 0.8957 (p0) cc_final: 0.8742 (p0) REVERT: A 110 TYR cc_start: 0.8954 (t80) cc_final: 0.8638 (t80) REVERT: A 111 MET cc_start: 0.7796 (ppp) cc_final: 0.7132 (ptm) REVERT: A 178 ASP cc_start: 0.8519 (t70) cc_final: 0.7792 (t70) REVERT: A 227 MET cc_start: 0.8770 (tpt) cc_final: 0.8369 (tpp) REVERT: A 229 ASP cc_start: 0.8656 (p0) cc_final: 0.7897 (p0) REVERT: A 240 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8415 (mm-30) REVERT: A 273 MET cc_start: 0.9140 (ttm) cc_final: 0.8879 (ttm) REVERT: A 278 LEU cc_start: 0.9131 (pp) cc_final: 0.8907 (pp) REVERT: A 305 ILE cc_start: 0.9122 (mt) cc_final: 0.8887 (mm) REVERT: B 16 PHE cc_start: 0.8492 (p90) cc_final: 0.8291 (p90) REVERT: B 65 ASN cc_start: 0.9186 (p0) cc_final: 0.8792 (p0) REVERT: B 132 SER cc_start: 0.9538 (m) cc_final: 0.9249 (p) REVERT: B 156 ASP cc_start: 0.8161 (m-30) cc_final: 0.7926 (t0) REVERT: B 157 HIS cc_start: 0.8028 (m170) cc_final: 0.7314 (m90) REVERT: B 160 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8697 (pt0) REVERT: B 189 LEU cc_start: 0.9014 (pt) cc_final: 0.8054 (tt) REVERT: B 192 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8765 (tmtt) REVERT: B 208 TYR cc_start: 0.8826 (m-10) cc_final: 0.8533 (m-10) REVERT: B 232 ASP cc_start: 0.8917 (m-30) cc_final: 0.8203 (m-30) REVERT: B 254 GLU cc_start: 0.7983 (pp20) cc_final: 0.7653 (pp20) REVERT: B 282 PHE cc_start: 0.8859 (m-80) cc_final: 0.8582 (m-10) REVERT: C 19 MET cc_start: 0.8617 (mmm) cc_final: 0.8319 (mmm) REVERT: C 41 CYS cc_start: 0.8066 (p) cc_final: 0.7809 (p) REVERT: C 68 ASP cc_start: 0.8319 (t70) cc_final: 0.7951 (t0) REVERT: C 123 LYS cc_start: 0.9015 (mtpm) cc_final: 0.8670 (tptp) REVERT: C 132 SER cc_start: 0.9343 (t) cc_final: 0.9090 (p) REVERT: C 157 HIS cc_start: 0.7258 (m170) cc_final: 0.6688 (m-70) REVERT: C 160 GLU cc_start: 0.8684 (pp20) cc_final: 0.8442 (pp20) REVERT: C 163 GLU cc_start: 0.9294 (tp30) cc_final: 0.9017 (tp30) REVERT: C 229 ASP cc_start: 0.8740 (p0) cc_final: 0.8103 (p0) REVERT: C 240 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8208 (mm-30) REVERT: C 259 MET cc_start: 0.9270 (mmt) cc_final: 0.8967 (mmp) REVERT: C 326 TRP cc_start: 0.7898 (m100) cc_final: 0.7458 (m100) REVERT: D 18 TRP cc_start: 0.8953 (m100) cc_final: 0.8562 (m100) REVERT: D 46 ASN cc_start: 0.9359 (t0) cc_final: 0.8119 (t0) REVERT: D 49 HIS cc_start: 0.8402 (m170) cc_final: 0.7828 (m-70) REVERT: D 111 MET cc_start: 0.7860 (tmt) cc_final: 0.7485 (tmm) REVERT: D 123 LYS cc_start: 0.9237 (mtpp) cc_final: 0.8881 (mmmm) REVERT: D 151 CYS cc_start: 0.8983 (m) cc_final: 0.8062 (m) REVERT: D 157 HIS cc_start: 0.8106 (m170) cc_final: 0.7518 (m170) REVERT: D 189 LEU cc_start: 0.9294 (pt) cc_final: 0.8339 (tt) REVERT: D 194 LEU cc_start: 0.9722 (tp) cc_final: 0.9117 (tp) REVERT: D 200 TYR cc_start: 0.8490 (m-80) cc_final: 0.8282 (m-10) REVERT: D 227 MET cc_start: 0.8816 (tpt) cc_final: 0.8409 (tpp) REVERT: D 244 CYS cc_start: 0.9214 (m) cc_final: 0.8499 (t) REVERT: D 305 ILE cc_start: 0.9035 (mt) cc_final: 0.8766 (mm) REVERT: E 5 LYS cc_start: 0.9215 (ttmp) cc_final: 0.8828 (ttmm) REVERT: E 64 ASN cc_start: 0.9266 (m-40) cc_final: 0.9052 (m-40) REVERT: E 65 ASN cc_start: 0.9301 (p0) cc_final: 0.9034 (p0) REVERT: E 68 ASP cc_start: 0.8101 (t70) cc_final: 0.7805 (t0) REVERT: E 76 ARG cc_start: 0.8706 (pmt100) cc_final: 0.7813 (ptt180) REVERT: E 132 SER cc_start: 0.9266 (m) cc_final: 0.9051 (p) REVERT: E 151 CYS cc_start: 0.9245 (m) cc_final: 0.8990 (m) REVERT: E 197 MET cc_start: 0.8978 (ttp) cc_final: 0.8474 (ttp) REVERT: E 253 ASP cc_start: 0.8830 (t70) cc_final: 0.8510 (t70) REVERT: E 261 GLU cc_start: 0.8593 (tm-30) cc_final: 0.7743 (tm-30) REVERT: E 262 ASN cc_start: 0.9467 (m-40) cc_final: 0.8841 (m-40) REVERT: E 273 MET cc_start: 0.8900 (ttm) cc_final: 0.8447 (ttm) outliers start: 28 outliers final: 8 residues processed: 430 average time/residue: 0.2628 time to fit residues: 156.8658 Evaluate side-chains 324 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 316 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 39 HIS A 166 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 HIS D 204 GLN E 50 HIS E 157 HIS E 166 HIS E 193 GLN E 204 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13085 Z= 0.249 Angle : 0.811 8.325 17760 Z= 0.417 Chirality : 0.046 0.197 2005 Planarity : 0.007 0.090 2315 Dihedral : 7.047 82.753 1795 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.29 % Allowed : 5.78 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.18), residues: 1625 helix: -1.49 (0.15), residues: 880 sheet: -1.59 (0.44), residues: 135 loop : -3.19 (0.20), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 146 HIS 0.004 0.001 HIS E 157 PHE 0.030 0.002 PHE A 306 TYR 0.016 0.002 TYR A 268 ARG 0.006 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 425 time to evaluate : 1.550 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: A 46 ASN cc_start: 0.9247 (t0) cc_final: 0.8912 (t0) REVERT: A 65 ASN cc_start: 0.9044 (p0) cc_final: 0.8727 (p0) REVERT: A 105 VAL cc_start: 0.9127 (t) cc_final: 0.8238 (t) REVERT: A 110 TYR cc_start: 0.8863 (t80) cc_final: 0.8591 (t80) REVERT: A 111 MET cc_start: 0.7701 (ppp) cc_final: 0.6928 (ptm) REVERT: A 169 ILE cc_start: 0.9655 (pt) cc_final: 0.9434 (pt) REVERT: A 178 ASP cc_start: 0.8408 (t70) cc_final: 0.7949 (t70) REVERT: A 197 MET cc_start: 0.9038 (mtp) cc_final: 0.7610 (mtp) REVERT: A 273 MET cc_start: 0.8841 (ttm) cc_final: 0.7925 (mtp) REVERT: A 282 PHE cc_start: 0.8780 (m-80) cc_final: 0.8578 (m-80) REVERT: A 287 PHE cc_start: 0.7941 (m-10) cc_final: 0.7667 (m-10) REVERT: A 305 ILE cc_start: 0.8994 (mt) cc_final: 0.8744 (mm) REVERT: B 1 MET cc_start: 0.7164 (ptp) cc_final: 0.6954 (ptm) REVERT: B 46 ASN cc_start: 0.9310 (t0) cc_final: 0.9098 (t0) REVERT: B 65 ASN cc_start: 0.9135 (p0) cc_final: 0.8794 (p0) REVERT: B 92 CYS cc_start: 0.8339 (t) cc_final: 0.8019 (m) REVERT: B 151 CYS cc_start: 0.9381 (m) cc_final: 0.8966 (m) REVERT: B 157 HIS cc_start: 0.7920 (m170) cc_final: 0.7156 (m-70) REVERT: B 160 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8636 (pt0) REVERT: B 189 LEU cc_start: 0.9064 (pt) cc_final: 0.8004 (tt) REVERT: B 192 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8551 (tmtt) REVERT: B 253 ASP cc_start: 0.8688 (t70) cc_final: 0.8446 (t70) REVERT: B 268 TYR cc_start: 0.8884 (t80) cc_final: 0.8636 (t80) REVERT: B 282 PHE cc_start: 0.8821 (m-80) cc_final: 0.8480 (m-10) REVERT: C 18 TRP cc_start: 0.8403 (m100) cc_final: 0.7556 (m100) REVERT: C 68 ASP cc_start: 0.8242 (t70) cc_final: 0.7819 (t0) REVERT: C 111 MET cc_start: 0.8021 (ppp) cc_final: 0.7724 (ppp) REVERT: C 123 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8560 (tppp) REVERT: C 157 HIS cc_start: 0.7328 (m170) cc_final: 0.6695 (m-70) REVERT: C 160 GLU cc_start: 0.8739 (pp20) cc_final: 0.8448 (pp20) REVERT: C 167 ASP cc_start: 0.8911 (p0) cc_final: 0.8592 (p0) REVERT: C 200 TYR cc_start: 0.8521 (m-80) cc_final: 0.8100 (m-80) REVERT: C 229 ASP cc_start: 0.8870 (p0) cc_final: 0.8664 (p0) REVERT: C 232 ASP cc_start: 0.8431 (m-30) cc_final: 0.8102 (m-30) REVERT: C 254 GLU cc_start: 0.8021 (pp20) cc_final: 0.7763 (pp20) REVERT: C 259 MET cc_start: 0.9113 (mmt) cc_final: 0.8837 (mmp) REVERT: C 326 TRP cc_start: 0.7952 (m100) cc_final: 0.7519 (m100) REVERT: D 1 MET cc_start: 0.7666 (ppp) cc_final: 0.7214 (ppp) REVERT: D 18 TRP cc_start: 0.9081 (m100) cc_final: 0.8273 (m100) REVERT: D 41 CYS cc_start: 0.7735 (p) cc_final: 0.7049 (p) REVERT: D 46 ASN cc_start: 0.9350 (t0) cc_final: 0.8585 (t0) REVERT: D 49 HIS cc_start: 0.8558 (m170) cc_final: 0.8146 (m-70) REVERT: D 78 ARG cc_start: 0.8694 (ttp-110) cc_final: 0.7977 (ttp-110) REVERT: D 92 CYS cc_start: 0.8727 (t) cc_final: 0.8390 (t) REVERT: D 111 MET cc_start: 0.8010 (ttt) cc_final: 0.6300 (ttt) REVERT: D 123 LYS cc_start: 0.9147 (mtpp) cc_final: 0.8894 (mmmm) REVERT: D 125 LEU cc_start: 0.9474 (mp) cc_final: 0.9244 (mp) REVERT: D 151 CYS cc_start: 0.8805 (m) cc_final: 0.8557 (m) REVERT: D 157 HIS cc_start: 0.8043 (m170) cc_final: 0.7592 (m170) REVERT: D 169 ILE cc_start: 0.9488 (pt) cc_final: 0.9235 (pt) REVERT: D 194 LEU cc_start: 0.9594 (tp) cc_final: 0.8815 (tp) REVERT: D 200 TYR cc_start: 0.8377 (m-80) cc_final: 0.8109 (m-10) REVERT: D 227 MET cc_start: 0.8468 (tpt) cc_final: 0.8154 (tpp) REVERT: D 238 LEU cc_start: 0.9720 (pp) cc_final: 0.9458 (pp) REVERT: D 244 CYS cc_start: 0.8939 (m) cc_final: 0.8336 (t) REVERT: D 260 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8592 (tm-30) REVERT: E 5 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8807 (ttmm) REVERT: E 16 PHE cc_start: 0.8016 (m-10) cc_final: 0.7738 (m-10) REVERT: E 42 TRP cc_start: 0.9074 (t60) cc_final: 0.8124 (t60) REVERT: E 46 ASN cc_start: 0.8951 (t0) cc_final: 0.8743 (t0) REVERT: E 65 ASN cc_start: 0.9272 (p0) cc_final: 0.8959 (p0) REVERT: E 92 CYS cc_start: 0.8713 (t) cc_final: 0.8409 (t) REVERT: E 111 MET cc_start: 0.8500 (ppp) cc_final: 0.8277 (ppp) REVERT: E 132 SER cc_start: 0.9317 (m) cc_final: 0.9067 (p) REVERT: E 151 CYS cc_start: 0.9182 (m) cc_final: 0.8320 (m) REVERT: E 169 ILE cc_start: 0.9555 (pt) cc_final: 0.9337 (pt) REVERT: E 178 ASP cc_start: 0.8752 (t70) cc_final: 0.8507 (t70) REVERT: E 200 TYR cc_start: 0.9115 (m-80) cc_final: 0.8670 (m-80) REVERT: E 201 MET cc_start: 0.8973 (mmp) cc_final: 0.8726 (mmp) REVERT: E 229 ASP cc_start: 0.8582 (p0) cc_final: 0.8353 (p0) REVERT: E 232 ASP cc_start: 0.8798 (m-30) cc_final: 0.8454 (m-30) REVERT: E 254 GLU cc_start: 0.8734 (pp20) cc_final: 0.8492 (pp20) REVERT: E 257 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8764 (tm-30) REVERT: E 261 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7932 (tm-30) REVERT: E 262 ASN cc_start: 0.9347 (m-40) cc_final: 0.8828 (m-40) REVERT: E 270 MET cc_start: 0.8959 (tpt) cc_final: 0.8624 (tpt) outliers start: 4 outliers final: 0 residues processed: 428 average time/residue: 0.2388 time to fit residues: 146.9783 Evaluate side-chains 355 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 103 GLN E 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13085 Z= 0.271 Angle : 0.795 8.565 17760 Z= 0.409 Chirality : 0.047 0.191 2005 Planarity : 0.006 0.063 2315 Dihedral : 6.670 79.489 1795 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.19), residues: 1625 helix: -0.83 (0.16), residues: 900 sheet: -1.40 (0.44), residues: 135 loop : -2.94 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 218 HIS 0.003 0.001 HIS E 157 PHE 0.025 0.002 PHE E 306 TYR 0.016 0.002 TYR A 268 ARG 0.011 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 1.616 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: A 16 PHE cc_start: 0.8155 (p90) cc_final: 0.7572 (p90) REVERT: A 46 ASN cc_start: 0.9272 (t0) cc_final: 0.8937 (t0) REVERT: A 65 ASN cc_start: 0.9154 (p0) cc_final: 0.8820 (p0) REVERT: A 110 TYR cc_start: 0.8932 (t80) cc_final: 0.8687 (t80) REVERT: A 111 MET cc_start: 0.7822 (ppp) cc_final: 0.7236 (ptm) REVERT: A 157 HIS cc_start: 0.8338 (m-70) cc_final: 0.7737 (m90) REVERT: A 178 ASP cc_start: 0.8521 (t70) cc_final: 0.8213 (t70) REVERT: A 242 ASP cc_start: 0.9065 (p0) cc_final: 0.8800 (p0) REVERT: A 270 MET cc_start: 0.8307 (mmm) cc_final: 0.7992 (mmm) REVERT: A 282 PHE cc_start: 0.8826 (m-80) cc_final: 0.8577 (m-80) REVERT: A 287 PHE cc_start: 0.7927 (m-10) cc_final: 0.7697 (m-10) REVERT: A 305 ILE cc_start: 0.8977 (mt) cc_final: 0.8738 (mm) REVERT: A 306 PHE cc_start: 0.8244 (p90) cc_final: 0.7885 (p90) REVERT: B 46 ASN cc_start: 0.9293 (t0) cc_final: 0.8929 (t0) REVERT: B 92 CYS cc_start: 0.8195 (t) cc_final: 0.7896 (m) REVERT: B 160 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8670 (mt-10) REVERT: B 189 LEU cc_start: 0.9121 (pt) cc_final: 0.8197 (tt) REVERT: B 192 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8644 (tmtt) REVERT: B 197 MET cc_start: 0.9250 (ttm) cc_final: 0.9019 (ttm) REVERT: B 200 TYR cc_start: 0.8085 (m-10) cc_final: 0.7367 (m-10) REVERT: B 253 ASP cc_start: 0.8718 (t70) cc_final: 0.8474 (t70) REVERT: B 268 TYR cc_start: 0.8905 (t80) cc_final: 0.8692 (t80) REVERT: B 278 LEU cc_start: 0.8854 (tt) cc_final: 0.8622 (tt) REVERT: B 282 PHE cc_start: 0.8792 (m-80) cc_final: 0.8405 (m-10) REVERT: C 18 TRP cc_start: 0.8460 (m100) cc_final: 0.7930 (m100) REVERT: C 19 MET cc_start: 0.8687 (mmp) cc_final: 0.8451 (mmm) REVERT: C 46 ASN cc_start: 0.9040 (t0) cc_final: 0.8814 (t0) REVERT: C 68 ASP cc_start: 0.8295 (t70) cc_final: 0.7830 (t0) REVERT: C 111 MET cc_start: 0.7984 (ppp) cc_final: 0.7589 (ppp) REVERT: C 123 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8551 (tppp) REVERT: C 157 HIS cc_start: 0.7519 (m170) cc_final: 0.6970 (m-70) REVERT: C 160 GLU cc_start: 0.8715 (pp20) cc_final: 0.8489 (pp20) REVERT: C 200 TYR cc_start: 0.8646 (m-80) cc_final: 0.7889 (m-80) REVERT: C 208 TYR cc_start: 0.8934 (m-10) cc_final: 0.8531 (m-80) REVERT: C 232 ASP cc_start: 0.8445 (m-30) cc_final: 0.8226 (m-30) REVERT: C 240 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8218 (mm-30) REVERT: C 259 MET cc_start: 0.9144 (mmt) cc_final: 0.8868 (mmp) REVERT: C 270 MET cc_start: 0.9074 (ttt) cc_final: 0.8643 (ttt) REVERT: C 326 TRP cc_start: 0.7888 (m100) cc_final: 0.7339 (m100) REVERT: D 1 MET cc_start: 0.7601 (ppp) cc_final: 0.7092 (ppp) REVERT: D 18 TRP cc_start: 0.9047 (m100) cc_final: 0.8513 (m100) REVERT: D 46 ASN cc_start: 0.9364 (t0) cc_final: 0.9100 (t0) REVERT: D 78 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.7948 (ttp-110) REVERT: D 111 MET cc_start: 0.7950 (ttt) cc_final: 0.6161 (ttt) REVERT: D 123 LYS cc_start: 0.9172 (mtpp) cc_final: 0.8875 (mmmm) REVERT: D 125 LEU cc_start: 0.9476 (mp) cc_final: 0.9261 (mp) REVERT: D 157 HIS cc_start: 0.8333 (m170) cc_final: 0.7908 (m170) REVERT: D 189 LEU cc_start: 0.9326 (pp) cc_final: 0.8646 (tt) REVERT: D 194 LEU cc_start: 0.9685 (tp) cc_final: 0.9008 (tp) REVERT: D 200 TYR cc_start: 0.8554 (m-80) cc_final: 0.8139 (m-10) REVERT: D 238 LEU cc_start: 0.9687 (pp) cc_final: 0.9429 (pp) REVERT: D 239 ASP cc_start: 0.9140 (t0) cc_final: 0.8920 (t70) REVERT: D 244 CYS cc_start: 0.9046 (m) cc_final: 0.8269 (t) REVERT: D 260 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8557 (tm-30) REVERT: D 275 MET cc_start: 0.8834 (mmt) cc_final: 0.8535 (mmm) REVERT: D 278 LEU cc_start: 0.9110 (tt) cc_final: 0.8717 (tt) REVERT: E 46 ASN cc_start: 0.8944 (t0) cc_final: 0.8744 (t0) REVERT: E 51 ASP cc_start: 0.8705 (m-30) cc_final: 0.8406 (t0) REVERT: E 65 ASN cc_start: 0.9257 (p0) cc_final: 0.8954 (p0) REVERT: E 111 MET cc_start: 0.8281 (ppp) cc_final: 0.7996 (ppp) REVERT: E 132 SER cc_start: 0.9384 (m) cc_final: 0.9093 (p) REVERT: E 169 ILE cc_start: 0.9577 (pt) cc_final: 0.9337 (pt) REVERT: E 211 LEU cc_start: 0.9428 (mp) cc_final: 0.9225 (tt) REVERT: E 229 ASP cc_start: 0.8690 (p0) cc_final: 0.8481 (p0) REVERT: E 234 LEU cc_start: 0.9636 (tp) cc_final: 0.9358 (tp) REVERT: E 251 MET cc_start: 0.8278 (tpp) cc_final: 0.7742 (mmt) REVERT: E 254 GLU cc_start: 0.8746 (pp20) cc_final: 0.8509 (pp20) REVERT: E 261 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8055 (tm-30) REVERT: E 262 ASN cc_start: 0.9409 (m-40) cc_final: 0.8594 (m110) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.2387 time to fit residues: 138.7713 Evaluate side-chains 332 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.8980 chunk 109 optimal weight: 0.0670 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13085 Z= 0.222 Angle : 0.784 9.281 17760 Z= 0.391 Chirality : 0.046 0.236 2005 Planarity : 0.006 0.057 2315 Dihedral : 6.517 78.821 1795 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.22 % Allowed : 4.84 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1625 helix: -0.25 (0.17), residues: 870 sheet: -1.23 (0.44), residues: 135 loop : -2.77 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 146 HIS 0.008 0.001 HIS B 157 PHE 0.025 0.002 PHE A 306 TYR 0.015 0.002 TYR A 268 ARG 0.008 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 414 time to evaluate : 1.598 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: A 16 PHE cc_start: 0.8076 (p90) cc_final: 0.7736 (p90) REVERT: A 46 ASN cc_start: 0.9272 (t0) cc_final: 0.8990 (t0) REVERT: A 65 ASN cc_start: 0.9200 (p0) cc_final: 0.8845 (p0) REVERT: A 110 TYR cc_start: 0.8771 (t80) cc_final: 0.8397 (t80) REVERT: A 176 LEU cc_start: 0.9341 (pt) cc_final: 0.9120 (pt) REVERT: A 178 ASP cc_start: 0.8495 (t70) cc_final: 0.8066 (t70) REVERT: A 242 ASP cc_start: 0.8975 (p0) cc_final: 0.8700 (p0) REVERT: A 273 MET cc_start: 0.8540 (mtp) cc_final: 0.8300 (mtm) REVERT: A 282 PHE cc_start: 0.8693 (m-80) cc_final: 0.8417 (m-80) REVERT: A 305 ILE cc_start: 0.8967 (mt) cc_final: 0.8729 (mm) REVERT: B 43 LEU cc_start: 0.9058 (tt) cc_final: 0.8736 (mp) REVERT: B 46 ASN cc_start: 0.9248 (t0) cc_final: 0.8907 (t0) REVERT: B 65 ASN cc_start: 0.8813 (p0) cc_final: 0.8192 (p0) REVERT: B 92 CYS cc_start: 0.8172 (t) cc_final: 0.7883 (m) REVERT: B 160 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8676 (mt-10) REVERT: B 189 LEU cc_start: 0.9073 (pt) cc_final: 0.8053 (tt) REVERT: B 192 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8657 (tttt) REVERT: B 197 MET cc_start: 0.9284 (ttm) cc_final: 0.8643 (tpp) REVERT: B 200 TYR cc_start: 0.7886 (m-10) cc_final: 0.7132 (m-10) REVERT: B 232 ASP cc_start: 0.8604 (m-30) cc_final: 0.8361 (m-30) REVERT: B 253 ASP cc_start: 0.8759 (t70) cc_final: 0.8485 (t70) REVERT: B 282 PHE cc_start: 0.8722 (m-80) cc_final: 0.8326 (m-10) REVERT: C 18 TRP cc_start: 0.8539 (m100) cc_final: 0.8070 (m100) REVERT: C 46 ASN cc_start: 0.9098 (t0) cc_final: 0.8773 (t0) REVERT: C 68 ASP cc_start: 0.8282 (t70) cc_final: 0.8056 (t0) REVERT: C 123 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8576 (tppp) REVERT: C 157 HIS cc_start: 0.7459 (m170) cc_final: 0.6937 (m-70) REVERT: C 160 GLU cc_start: 0.8731 (pp20) cc_final: 0.8484 (pp20) REVERT: C 176 LEU cc_start: 0.9390 (pp) cc_final: 0.9188 (pp) REVERT: C 208 TYR cc_start: 0.8771 (m-10) cc_final: 0.8466 (m-80) REVERT: C 229 ASP cc_start: 0.8878 (p0) cc_final: 0.8638 (p0) REVERT: C 232 ASP cc_start: 0.8441 (m-30) cc_final: 0.8216 (m-30) REVERT: C 248 THR cc_start: 0.9181 (t) cc_final: 0.8957 (t) REVERT: C 259 MET cc_start: 0.9038 (mmt) cc_final: 0.8824 (mmp) REVERT: C 266 ARG cc_start: 0.8267 (mmp80) cc_final: 0.8049 (mmp-170) REVERT: C 270 MET cc_start: 0.8891 (ttt) cc_final: 0.8447 (ttt) REVERT: C 326 TRP cc_start: 0.7890 (m100) cc_final: 0.7427 (m100) REVERT: D 1 MET cc_start: 0.7567 (ppp) cc_final: 0.7072 (ppp) REVERT: D 18 TRP cc_start: 0.8925 (m100) cc_final: 0.8475 (m100) REVERT: D 46 ASN cc_start: 0.9358 (t0) cc_final: 0.9065 (t0) REVERT: D 78 ARG cc_start: 0.8543 (ttp-110) cc_final: 0.8112 (ttp-110) REVERT: D 111 MET cc_start: 0.7828 (ttt) cc_final: 0.6815 (ttt) REVERT: D 123 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8808 (mmmm) REVERT: D 164 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8779 (pm20) REVERT: D 189 LEU cc_start: 0.9295 (pp) cc_final: 0.8604 (tt) REVERT: D 194 LEU cc_start: 0.9686 (tp) cc_final: 0.8965 (tp) REVERT: D 227 MET cc_start: 0.8372 (tpp) cc_final: 0.8073 (tpt) REVERT: D 244 CYS cc_start: 0.8984 (m) cc_final: 0.8367 (t) REVERT: D 278 LEU cc_start: 0.9158 (tt) cc_final: 0.8352 (tt) REVERT: E 46 ASN cc_start: 0.8930 (t0) cc_final: 0.8718 (t0) REVERT: E 65 ASN cc_start: 0.9237 (p0) cc_final: 0.8908 (p0) REVERT: E 92 CYS cc_start: 0.8458 (t) cc_final: 0.8199 (t) REVERT: E 111 MET cc_start: 0.8227 (ppp) cc_final: 0.7962 (ppp) REVERT: E 132 SER cc_start: 0.9422 (m) cc_final: 0.9091 (p) REVERT: E 163 GLU cc_start: 0.8539 (tp30) cc_final: 0.8291 (tp30) REVERT: E 169 ILE cc_start: 0.9593 (pt) cc_final: 0.9315 (pt) REVERT: E 197 MET cc_start: 0.9136 (ttm) cc_final: 0.8195 (ttm) REVERT: E 229 ASP cc_start: 0.8671 (p0) cc_final: 0.8467 (p0) REVERT: E 261 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8115 (tm-30) REVERT: E 262 ASN cc_start: 0.9343 (m-40) cc_final: 0.8562 (m110) outliers start: 3 outliers final: 0 residues processed: 416 average time/residue: 0.2358 time to fit residues: 141.4450 Evaluate side-chains 339 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.0010 chunk 138 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13085 Z= 0.235 Angle : 0.791 9.302 17760 Z= 0.395 Chirality : 0.046 0.195 2005 Planarity : 0.006 0.055 2315 Dihedral : 6.416 78.133 1795 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1625 helix: -0.08 (0.17), residues: 870 sheet: -1.06 (0.45), residues: 135 loop : -2.61 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 218 HIS 0.008 0.001 HIS B 157 PHE 0.038 0.002 PHE C 306 TYR 0.014 0.002 TYR D 110 ARG 0.013 0.001 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 1.621 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: A 46 ASN cc_start: 0.9264 (t0) cc_final: 0.8956 (t0) REVERT: A 65 ASN cc_start: 0.9146 (p0) cc_final: 0.8809 (p0) REVERT: A 110 TYR cc_start: 0.8861 (t80) cc_final: 0.8517 (t80) REVERT: A 169 ILE cc_start: 0.9757 (pt) cc_final: 0.9499 (pt) REVERT: A 176 LEU cc_start: 0.9319 (pt) cc_final: 0.9051 (pt) REVERT: A 178 ASP cc_start: 0.8561 (t70) cc_final: 0.8145 (t70) REVERT: A 282 PHE cc_start: 0.8711 (m-80) cc_final: 0.8430 (m-80) REVERT: A 283 LEU cc_start: 0.8918 (pp) cc_final: 0.8669 (pp) REVERT: A 305 ILE cc_start: 0.8952 (mt) cc_final: 0.8731 (mm) REVERT: A 326 TRP cc_start: 0.7903 (m100) cc_final: 0.7692 (m100) REVERT: B 46 ASN cc_start: 0.9207 (t0) cc_final: 0.8992 (t0) REVERT: B 92 CYS cc_start: 0.8174 (t) cc_final: 0.7910 (m) REVERT: B 93 ILE cc_start: 0.7589 (pt) cc_final: 0.7026 (pt) REVERT: B 107 MET cc_start: 0.8684 (tmm) cc_final: 0.8377 (tmm) REVERT: B 134 LEU cc_start: 0.9404 (pp) cc_final: 0.9202 (pp) REVERT: B 160 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8708 (mt-10) REVERT: B 189 LEU cc_start: 0.9008 (pt) cc_final: 0.8075 (tt) REVERT: B 192 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8599 (tttm) REVERT: B 197 MET cc_start: 0.9085 (ttm) cc_final: 0.8614 (tpp) REVERT: B 200 TYR cc_start: 0.7838 (m-10) cc_final: 0.7215 (m-10) REVERT: B 232 ASP cc_start: 0.8543 (m-30) cc_final: 0.8321 (m-30) REVERT: B 253 ASP cc_start: 0.8661 (t70) cc_final: 0.8314 (t70) REVERT: B 257 GLN cc_start: 0.8839 (pp30) cc_final: 0.7557 (tm-30) REVERT: B 282 PHE cc_start: 0.8789 (m-80) cc_final: 0.8564 (m-10) REVERT: C 18 TRP cc_start: 0.8543 (m100) cc_final: 0.8231 (m100) REVERT: C 46 ASN cc_start: 0.9084 (t0) cc_final: 0.8766 (t0) REVERT: C 68 ASP cc_start: 0.8294 (t70) cc_final: 0.7849 (t0) REVERT: C 157 HIS cc_start: 0.7570 (m170) cc_final: 0.7010 (m-70) REVERT: C 176 LEU cc_start: 0.9394 (pp) cc_final: 0.9145 (pp) REVERT: C 208 TYR cc_start: 0.8730 (m-10) cc_final: 0.8318 (m-80) REVERT: C 251 MET cc_start: 0.8471 (mmt) cc_final: 0.7731 (mmt) REVERT: C 254 GLU cc_start: 0.8062 (pp20) cc_final: 0.7819 (pp20) REVERT: C 259 MET cc_start: 0.9154 (mmt) cc_final: 0.8924 (mmp) REVERT: C 266 ARG cc_start: 0.8255 (mmp80) cc_final: 0.8053 (mmp-170) REVERT: C 268 TYR cc_start: 0.8953 (t80) cc_final: 0.8741 (t80) REVERT: C 270 MET cc_start: 0.8908 (ttt) cc_final: 0.8577 (ttp) REVERT: D 1 MET cc_start: 0.7505 (ppp) cc_final: 0.7023 (ppp) REVERT: D 18 TRP cc_start: 0.8914 (m100) cc_final: 0.8464 (m100) REVERT: D 46 ASN cc_start: 0.9386 (t0) cc_final: 0.9088 (t0) REVERT: D 78 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8123 (ttp-110) REVERT: D 111 MET cc_start: 0.7810 (ttt) cc_final: 0.7148 (ttt) REVERT: D 123 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8853 (mmmm) REVERT: D 189 LEU cc_start: 0.9267 (pp) cc_final: 0.8606 (tt) REVERT: D 194 LEU cc_start: 0.9673 (tp) cc_final: 0.9037 (tp) REVERT: D 227 MET cc_start: 0.8469 (tpp) cc_final: 0.8029 (tpt) REVERT: D 244 CYS cc_start: 0.8974 (m) cc_final: 0.8374 (t) REVERT: D 245 ILE cc_start: 0.9264 (pt) cc_final: 0.9023 (pt) REVERT: D 278 LEU cc_start: 0.9070 (tt) cc_final: 0.8483 (tt) REVERT: D 282 PHE cc_start: 0.8732 (m-80) cc_final: 0.8509 (m-80) REVERT: E 5 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8840 (ttmm) REVERT: E 65 ASN cc_start: 0.9173 (p0) cc_final: 0.8832 (p0) REVERT: E 111 MET cc_start: 0.8375 (ppp) cc_final: 0.8089 (ppp) REVERT: E 132 SER cc_start: 0.9417 (m) cc_final: 0.9150 (p) REVERT: E 169 ILE cc_start: 0.9595 (pt) cc_final: 0.9358 (pt) REVERT: E 229 ASP cc_start: 0.8780 (p0) cc_final: 0.8562 (p0) REVERT: E 251 MET cc_start: 0.8652 (mmm) cc_final: 0.8106 (mmt) REVERT: E 261 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8038 (tm-30) REVERT: E 262 ASN cc_start: 0.9315 (m-40) cc_final: 0.8741 (m-40) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.2220 time to fit residues: 135.7278 Evaluate side-chains 341 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13085 Z= 0.292 Angle : 0.812 9.824 17760 Z= 0.412 Chirality : 0.048 0.225 2005 Planarity : 0.006 0.057 2315 Dihedral : 6.389 78.395 1795 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1625 helix: 0.10 (0.17), residues: 880 sheet: -1.29 (0.44), residues: 140 loop : -2.48 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 146 HIS 0.010 0.001 HIS B 157 PHE 0.029 0.003 PHE B 16 TYR 0.029 0.002 TYR E 208 ARG 0.009 0.001 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 1.484 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: A 46 ASN cc_start: 0.9264 (t0) cc_final: 0.8867 (t0) REVERT: A 65 ASN cc_start: 0.9176 (p0) cc_final: 0.8840 (p0) REVERT: A 107 MET cc_start: 0.9073 (tmm) cc_final: 0.8800 (tmm) REVERT: A 110 TYR cc_start: 0.8843 (t80) cc_final: 0.8367 (t80) REVERT: A 169 ILE cc_start: 0.9764 (pt) cc_final: 0.9517 (pt) REVERT: A 176 LEU cc_start: 0.9331 (pt) cc_final: 0.9066 (pt) REVERT: A 178 ASP cc_start: 0.8562 (t70) cc_final: 0.8297 (t70) REVERT: A 282 PHE cc_start: 0.8741 (m-80) cc_final: 0.8470 (m-80) REVERT: A 305 ILE cc_start: 0.8981 (mt) cc_final: 0.8767 (mm) REVERT: B 46 ASN cc_start: 0.9241 (t0) cc_final: 0.8992 (t0) REVERT: B 92 CYS cc_start: 0.8288 (t) cc_final: 0.8078 (m) REVERT: B 134 LEU cc_start: 0.9488 (pp) cc_final: 0.9277 (pp) REVERT: B 160 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8786 (mt-10) REVERT: B 189 LEU cc_start: 0.9013 (pt) cc_final: 0.8081 (tt) REVERT: B 192 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8683 (tttm) REVERT: B 197 MET cc_start: 0.9090 (ttm) cc_final: 0.8557 (tpp) REVERT: B 232 ASP cc_start: 0.8710 (m-30) cc_final: 0.8459 (m-30) REVERT: B 254 GLU cc_start: 0.8672 (tp30) cc_final: 0.8465 (tp30) REVERT: B 282 PHE cc_start: 0.8738 (m-80) cc_final: 0.8380 (m-10) REVERT: C 18 TRP cc_start: 0.8605 (m100) cc_final: 0.8309 (m100) REVERT: C 46 ASN cc_start: 0.9076 (t0) cc_final: 0.8799 (t0) REVERT: C 68 ASP cc_start: 0.8331 (t70) cc_final: 0.7895 (t0) REVERT: C 176 LEU cc_start: 0.9410 (pp) cc_final: 0.9162 (pp) REVERT: C 208 TYR cc_start: 0.8822 (m-10) cc_final: 0.8472 (m-80) REVERT: C 229 ASP cc_start: 0.9087 (p0) cc_final: 0.8831 (p0) REVERT: C 232 ASP cc_start: 0.8466 (m-30) cc_final: 0.8265 (m-30) REVERT: C 251 MET cc_start: 0.8231 (mmt) cc_final: 0.7576 (mmt) REVERT: C 254 GLU cc_start: 0.8572 (pp20) cc_final: 0.8264 (pp20) REVERT: C 259 MET cc_start: 0.9078 (mmt) cc_final: 0.8876 (mmp) REVERT: C 270 MET cc_start: 0.8924 (ttt) cc_final: 0.8548 (ttp) REVERT: C 275 MET cc_start: 0.8295 (mmp) cc_final: 0.8059 (mmp) REVERT: C 326 TRP cc_start: 0.7950 (m100) cc_final: 0.6401 (m100) REVERT: D 1 MET cc_start: 0.7610 (ppp) cc_final: 0.7075 (ppp) REVERT: D 18 TRP cc_start: 0.8861 (m100) cc_final: 0.8551 (m100) REVERT: D 46 ASN cc_start: 0.9362 (t0) cc_final: 0.9105 (t0) REVERT: D 65 ASN cc_start: 0.9082 (p0) cc_final: 0.8838 (p0) REVERT: D 78 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8223 (ttp-110) REVERT: D 111 MET cc_start: 0.7940 (ttt) cc_final: 0.7091 (ttt) REVERT: D 123 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8785 (mmmm) REVERT: D 189 LEU cc_start: 0.9314 (pp) cc_final: 0.8689 (tt) REVERT: D 194 LEU cc_start: 0.9675 (tp) cc_final: 0.9070 (tp) REVERT: D 227 MET cc_start: 0.8499 (tpp) cc_final: 0.8023 (tpt) REVERT: D 244 CYS cc_start: 0.9019 (m) cc_final: 0.8404 (t) REVERT: D 270 MET cc_start: 0.8983 (ttt) cc_final: 0.8704 (ttt) REVERT: D 278 LEU cc_start: 0.9236 (tt) cc_final: 0.8744 (tt) REVERT: D 282 PHE cc_start: 0.8728 (m-80) cc_final: 0.8493 (m-80) REVERT: E 5 LYS cc_start: 0.9171 (ttmm) cc_final: 0.8885 (ttmm) REVERT: E 46 ASN cc_start: 0.9010 (t0) cc_final: 0.8776 (t0) REVERT: E 65 ASN cc_start: 0.9086 (p0) cc_final: 0.8553 (p0) REVERT: E 111 MET cc_start: 0.8494 (ppp) cc_final: 0.8203 (ppp) REVERT: E 132 SER cc_start: 0.9490 (m) cc_final: 0.9186 (p) REVERT: E 169 ILE cc_start: 0.9645 (pt) cc_final: 0.9345 (pt) REVERT: E 234 LEU cc_start: 0.9566 (tp) cc_final: 0.9331 (tp) REVERT: E 251 MET cc_start: 0.8796 (mmm) cc_final: 0.8290 (mmt) REVERT: E 257 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8806 (tm-30) REVERT: E 261 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8167 (tm-30) REVERT: E 262 ASN cc_start: 0.9360 (m-40) cc_final: 0.8529 (m110) REVERT: E 270 MET cc_start: 0.8957 (tpt) cc_final: 0.8685 (tpt) REVERT: E 273 MET cc_start: 0.8574 (ttm) cc_final: 0.8245 (ttm) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.2246 time to fit residues: 129.3833 Evaluate side-chains 330 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.9990 chunk 17 optimal weight: 0.0770 chunk 88 optimal weight: 0.6980 chunk 113 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13085 Z= 0.213 Angle : 0.812 11.152 17760 Z= 0.399 Chirality : 0.047 0.210 2005 Planarity : 0.006 0.107 2315 Dihedral : 6.333 78.265 1795 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1625 helix: 0.17 (0.17), residues: 880 sheet: -1.05 (0.45), residues: 140 loop : -2.41 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 218 HIS 0.014 0.001 HIS A 157 PHE 0.041 0.002 PHE C 306 TYR 0.022 0.002 TYR B 110 ARG 0.010 0.000 ARG D 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 1.505 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: A 46 ASN cc_start: 0.9271 (t0) cc_final: 0.8906 (t0) REVERT: A 65 ASN cc_start: 0.9094 (p0) cc_final: 0.8827 (p0) REVERT: A 110 TYR cc_start: 0.8690 (t80) cc_final: 0.8209 (t80) REVERT: A 169 ILE cc_start: 0.9793 (pt) cc_final: 0.9551 (pt) REVERT: A 176 LEU cc_start: 0.9254 (pt) cc_final: 0.8936 (pt) REVERT: A 178 ASP cc_start: 0.8451 (t70) cc_final: 0.7977 (t70) REVERT: A 282 PHE cc_start: 0.8717 (m-80) cc_final: 0.8440 (m-80) REVERT: A 283 LEU cc_start: 0.8793 (pp) cc_final: 0.8592 (pp) REVERT: A 305 ILE cc_start: 0.8955 (mt) cc_final: 0.8745 (mm) REVERT: B 41 CYS cc_start: 0.7341 (m) cc_final: 0.7096 (m) REVERT: B 46 ASN cc_start: 0.9311 (t0) cc_final: 0.8822 (t0) REVERT: B 92 CYS cc_start: 0.8197 (t) cc_final: 0.7903 (m) REVERT: B 107 MET cc_start: 0.8785 (tmm) cc_final: 0.8407 (tmm) REVERT: B 160 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8781 (mt-10) REVERT: B 192 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8511 (tttt) REVERT: B 197 MET cc_start: 0.9120 (ttm) cc_final: 0.8566 (ttm) REVERT: B 200 TYR cc_start: 0.8206 (m-80) cc_final: 0.7510 (m-80) REVERT: B 251 MET cc_start: 0.7911 (mmt) cc_final: 0.7533 (mmt) REVERT: B 275 MET cc_start: 0.8614 (tpp) cc_final: 0.7776 (tpp) REVERT: B 282 PHE cc_start: 0.8811 (m-80) cc_final: 0.8608 (m-10) REVERT: C 46 ASN cc_start: 0.9099 (t0) cc_final: 0.8572 (t0) REVERT: C 68 ASP cc_start: 0.8325 (t70) cc_final: 0.8092 (t0) REVERT: C 200 TYR cc_start: 0.8709 (m-80) cc_final: 0.8156 (m-80) REVERT: C 208 TYR cc_start: 0.8746 (m-10) cc_final: 0.8367 (m-80) REVERT: C 229 ASP cc_start: 0.9071 (p0) cc_final: 0.8804 (p0) REVERT: C 232 ASP cc_start: 0.8294 (m-30) cc_final: 0.8089 (m-30) REVERT: C 251 MET cc_start: 0.8110 (mmt) cc_final: 0.7612 (mmt) REVERT: C 259 MET cc_start: 0.9098 (mmt) cc_final: 0.8888 (mmp) REVERT: C 270 MET cc_start: 0.8902 (ttt) cc_final: 0.8485 (ttp) REVERT: C 275 MET cc_start: 0.8277 (mmp) cc_final: 0.7983 (mmp) REVERT: C 326 TRP cc_start: 0.7960 (m100) cc_final: 0.7470 (m100) REVERT: D 1 MET cc_start: 0.7591 (ppp) cc_final: 0.7068 (ppp) REVERT: D 18 TRP cc_start: 0.8717 (m100) cc_final: 0.8321 (m100) REVERT: D 46 ASN cc_start: 0.9331 (t0) cc_final: 0.9050 (t0) REVERT: D 78 ARG cc_start: 0.8566 (ttp-110) cc_final: 0.8204 (ttp-110) REVERT: D 123 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8788 (mmmm) REVERT: D 169 ILE cc_start: 0.9547 (pt) cc_final: 0.9319 (pt) REVERT: D 189 LEU cc_start: 0.9310 (pp) cc_final: 0.8683 (tt) REVERT: D 194 LEU cc_start: 0.9718 (tp) cc_final: 0.9251 (tp) REVERT: D 200 TYR cc_start: 0.8466 (m-80) cc_final: 0.8228 (m-80) REVERT: D 201 MET cc_start: 0.8107 (mmt) cc_final: 0.7654 (mmt) REVERT: D 227 MET cc_start: 0.8562 (tpp) cc_final: 0.8012 (tpt) REVERT: D 232 ASP cc_start: 0.8305 (p0) cc_final: 0.8104 (p0) REVERT: D 244 CYS cc_start: 0.8939 (m) cc_final: 0.8379 (t) REVERT: D 278 LEU cc_start: 0.9211 (tt) cc_final: 0.8586 (tt) REVERT: D 282 PHE cc_start: 0.8678 (m-80) cc_final: 0.8465 (m-80) REVERT: E 5 LYS cc_start: 0.9131 (ttmm) cc_final: 0.8834 (ttmm) REVERT: E 46 ASN cc_start: 0.8972 (t0) cc_final: 0.8763 (t0) REVERT: E 65 ASN cc_start: 0.9036 (p0) cc_final: 0.8537 (p0) REVERT: E 111 MET cc_start: 0.8050 (ppp) cc_final: 0.7680 (ppp) REVERT: E 132 SER cc_start: 0.9458 (m) cc_final: 0.9118 (p) REVERT: E 169 ILE cc_start: 0.9587 (pt) cc_final: 0.9282 (pt) REVERT: E 208 TYR cc_start: 0.8784 (m-10) cc_final: 0.8334 (m-10) REVERT: E 229 ASP cc_start: 0.8752 (p0) cc_final: 0.8467 (p0) REVERT: E 251 MET cc_start: 0.8661 (mmm) cc_final: 0.8143 (mmt) REVERT: E 261 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8000 (tm-30) REVERT: E 262 ASN cc_start: 0.9251 (m-40) cc_final: 0.8653 (m-40) REVERT: E 273 MET cc_start: 0.8395 (ttm) cc_final: 0.8102 (ttm) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.2180 time to fit residues: 129.8360 Evaluate side-chains 331 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 0.0060 chunk 92 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 13085 Z= 0.419 Angle : 0.916 9.845 17760 Z= 0.472 Chirality : 0.051 0.200 2005 Planarity : 0.007 0.135 2315 Dihedral : 6.571 79.509 1795 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -1.70 (0.20), residues: 1625 helix: -0.17 (0.17), residues: 905 sheet: -1.64 (0.40), residues: 165 loop : -2.48 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 146 HIS 0.009 0.002 HIS B 157 PHE 0.028 0.003 PHE D 306 TYR 0.020 0.002 TYR D 110 ARG 0.014 0.001 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.494 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: A 46 ASN cc_start: 0.9237 (t0) cc_final: 0.8869 (t0) REVERT: A 65 ASN cc_start: 0.9237 (p0) cc_final: 0.8876 (p0) REVERT: A 107 MET cc_start: 0.9161 (tmm) cc_final: 0.8784 (tmm) REVERT: A 169 ILE cc_start: 0.9743 (pt) cc_final: 0.9474 (pt) REVERT: A 176 LEU cc_start: 0.9315 (pt) cc_final: 0.9007 (pt) REVERT: A 178 ASP cc_start: 0.8720 (t70) cc_final: 0.8331 (t70) REVERT: A 270 MET cc_start: 0.8876 (mmm) cc_final: 0.8670 (mmm) REVERT: A 273 MET cc_start: 0.8704 (mtp) cc_final: 0.8144 (mtp) REVERT: A 305 ILE cc_start: 0.9098 (mt) cc_final: 0.8898 (mm) REVERT: B 1 MET cc_start: 0.5107 (ppp) cc_final: 0.3906 (ppp) REVERT: B 41 CYS cc_start: 0.7606 (m) cc_final: 0.7320 (m) REVERT: B 92 CYS cc_start: 0.8290 (t) cc_final: 0.7974 (m) REVERT: B 107 MET cc_start: 0.8977 (tmm) cc_final: 0.8662 (tmm) REVERT: B 160 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8831 (mt-10) REVERT: B 189 LEU cc_start: 0.9133 (pt) cc_final: 0.8360 (tt) REVERT: B 192 LYS cc_start: 0.9271 (ttmm) cc_final: 0.8845 (tttt) REVERT: B 197 MET cc_start: 0.9320 (ttm) cc_final: 0.9058 (ttm) REVERT: B 229 ASP cc_start: 0.8767 (p0) cc_final: 0.8512 (p0) REVERT: B 232 ASP cc_start: 0.8669 (m-30) cc_final: 0.8288 (m-30) REVERT: B 278 LEU cc_start: 0.8885 (tt) cc_final: 0.8663 (tt) REVERT: B 282 PHE cc_start: 0.8734 (m-80) cc_final: 0.8381 (m-10) REVERT: C 18 TRP cc_start: 0.8631 (m100) cc_final: 0.8184 (m100) REVERT: C 46 ASN cc_start: 0.9144 (t0) cc_final: 0.8864 (t0) REVERT: C 68 ASP cc_start: 0.8412 (t70) cc_final: 0.7905 (t0) REVERT: C 107 MET cc_start: 0.9122 (tmm) cc_final: 0.8912 (tmm) REVERT: C 163 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8933 (tp30) REVERT: C 176 LEU cc_start: 0.9399 (pp) cc_final: 0.9163 (pp) REVERT: C 229 ASP cc_start: 0.9140 (p0) cc_final: 0.8914 (p0) REVERT: C 257 GLN cc_start: 0.9268 (pp30) cc_final: 0.9066 (pp30) REVERT: C 270 MET cc_start: 0.8874 (ttt) cc_final: 0.8368 (ttm) REVERT: C 326 TRP cc_start: 0.8107 (m100) cc_final: 0.6506 (m100) REVERT: D 1 MET cc_start: 0.7647 (ppp) cc_final: 0.7112 (ppp) REVERT: D 18 TRP cc_start: 0.8734 (m100) cc_final: 0.8512 (m100) REVERT: D 78 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.7963 (ttp-110) REVERT: D 92 CYS cc_start: 0.8398 (t) cc_final: 0.8121 (t) REVERT: D 111 MET cc_start: 0.8397 (ttp) cc_final: 0.8110 (tmm) REVERT: D 169 ILE cc_start: 0.9625 (pt) cc_final: 0.9409 (pt) REVERT: D 189 LEU cc_start: 0.9357 (pp) cc_final: 0.8804 (tt) REVERT: D 194 LEU cc_start: 0.9706 (tp) cc_final: 0.9133 (tp) REVERT: D 200 TYR cc_start: 0.8432 (m-80) cc_final: 0.8043 (m-80) REVERT: D 244 CYS cc_start: 0.9014 (m) cc_final: 0.8443 (t) REVERT: D 275 MET cc_start: 0.8856 (mmp) cc_final: 0.8129 (mmt) REVERT: D 278 LEU cc_start: 0.9191 (tt) cc_final: 0.8729 (tt) REVERT: D 282 PHE cc_start: 0.8738 (m-80) cc_final: 0.8521 (m-80) REVERT: E 5 LYS cc_start: 0.9292 (ttmm) cc_final: 0.8990 (ttmm) REVERT: E 65 ASN cc_start: 0.9122 (p0) cc_final: 0.8618 (p0) REVERT: E 111 MET cc_start: 0.8159 (ppp) cc_final: 0.7794 (ppp) REVERT: E 129 ASP cc_start: 0.9055 (t70) cc_final: 0.8798 (t0) REVERT: E 132 SER cc_start: 0.9527 (m) cc_final: 0.9175 (p) REVERT: E 169 ILE cc_start: 0.9657 (pt) cc_final: 0.9313 (pt) REVERT: E 197 MET cc_start: 0.9282 (ttm) cc_final: 0.8612 (ttm) REVERT: E 208 TYR cc_start: 0.8818 (m-10) cc_final: 0.8406 (m-10) REVERT: E 229 ASP cc_start: 0.8822 (p0) cc_final: 0.8597 (p0) REVERT: E 257 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8816 (tm-30) REVERT: E 261 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8110 (tm-30) REVERT: E 262 ASN cc_start: 0.9426 (m-40) cc_final: 0.8882 (m-40) REVERT: E 268 TYR cc_start: 0.8186 (t80) cc_final: 0.7840 (t80) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2263 time to fit residues: 123.8453 Evaluate side-chains 309 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13085 Z= 0.235 Angle : 0.851 11.943 17760 Z= 0.416 Chirality : 0.048 0.256 2005 Planarity : 0.006 0.109 2315 Dihedral : 6.398 78.926 1795 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1625 helix: -0.02 (0.17), residues: 900 sheet: -1.45 (0.41), residues: 165 loop : -2.32 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 146 HIS 0.007 0.001 HIS A 157 PHE 0.048 0.003 PHE C 306 TYR 0.022 0.002 TYR B 110 ARG 0.015 0.001 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 1.720 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: A 46 ASN cc_start: 0.9267 (t0) cc_final: 0.8812 (t0) REVERT: A 65 ASN cc_start: 0.9163 (p0) cc_final: 0.8828 (p0) REVERT: A 107 MET cc_start: 0.9047 (tmm) cc_final: 0.8819 (tmm) REVERT: A 169 ILE cc_start: 0.9752 (pt) cc_final: 0.9501 (pt) REVERT: A 178 ASP cc_start: 0.8555 (t70) cc_final: 0.8100 (t70) REVERT: A 282 PHE cc_start: 0.8657 (m-80) cc_final: 0.8417 (m-80) REVERT: A 305 ILE cc_start: 0.9010 (mt) cc_final: 0.8802 (mm) REVERT: B 41 CYS cc_start: 0.7550 (m) cc_final: 0.7148 (m) REVERT: B 46 ASN cc_start: 0.9291 (t0) cc_final: 0.8868 (t0) REVERT: B 92 CYS cc_start: 0.8416 (t) cc_final: 0.8053 (m) REVERT: B 107 MET cc_start: 0.8876 (tmm) cc_final: 0.8635 (tmm) REVERT: B 134 LEU cc_start: 0.9469 (pp) cc_final: 0.9144 (pp) REVERT: B 160 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8842 (mt-10) REVERT: B 189 LEU cc_start: 0.9026 (pt) cc_final: 0.8172 (tt) REVERT: B 192 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8643 (tttm) REVERT: B 232 ASP cc_start: 0.8508 (m-30) cc_final: 0.8165 (t0) REVERT: B 251 MET cc_start: 0.8021 (mmt) cc_final: 0.7756 (mmt) REVERT: B 268 TYR cc_start: 0.9054 (t80) cc_final: 0.8826 (t80) REVERT: B 282 PHE cc_start: 0.8779 (m-80) cc_final: 0.8442 (m-10) REVERT: C 18 TRP cc_start: 0.8637 (m100) cc_final: 0.8197 (m100) REVERT: C 46 ASN cc_start: 0.9122 (t0) cc_final: 0.8806 (t0) REVERT: C 68 ASP cc_start: 0.8278 (t70) cc_final: 0.8003 (t0) REVERT: C 176 LEU cc_start: 0.9295 (pp) cc_final: 0.9091 (pp) REVERT: C 200 TYR cc_start: 0.8711 (m-80) cc_final: 0.8130 (m-80) REVERT: C 201 MET cc_start: 0.8606 (mmp) cc_final: 0.7616 (mmp) REVERT: C 219 MET cc_start: 0.8510 (mtm) cc_final: 0.8250 (mtm) REVERT: C 229 ASP cc_start: 0.9098 (p0) cc_final: 0.8810 (p0) REVERT: C 251 MET cc_start: 0.8194 (mmt) cc_final: 0.7484 (mmt) REVERT: C 254 GLU cc_start: 0.8308 (pp20) cc_final: 0.7977 (pp20) REVERT: C 270 MET cc_start: 0.8879 (ttt) cc_final: 0.8505 (mtp) REVERT: C 326 TRP cc_start: 0.7884 (m100) cc_final: 0.6148 (m100) REVERT: D 1 MET cc_start: 0.7591 (ppp) cc_final: 0.7047 (ppp) REVERT: D 18 TRP cc_start: 0.8735 (m100) cc_final: 0.8352 (m100) REVERT: D 46 ASN cc_start: 0.9355 (t0) cc_final: 0.9125 (t0) REVERT: D 78 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8116 (ttp-110) REVERT: D 169 ILE cc_start: 0.9567 (pt) cc_final: 0.9295 (pt) REVERT: D 181 ILE cc_start: 0.9379 (tt) cc_final: 0.9148 (tt) REVERT: D 189 LEU cc_start: 0.9299 (pp) cc_final: 0.8740 (tt) REVERT: D 194 LEU cc_start: 0.9698 (tp) cc_final: 0.9224 (tp) REVERT: D 200 TYR cc_start: 0.8337 (m-80) cc_final: 0.7988 (m-80) REVERT: D 244 CYS cc_start: 0.8903 (m) cc_final: 0.8311 (t) REVERT: D 278 LEU cc_start: 0.9203 (tt) cc_final: 0.8687 (tt) REVERT: D 282 PHE cc_start: 0.8702 (m-80) cc_final: 0.8425 (m-80) REVERT: E 5 LYS cc_start: 0.9227 (ttmm) cc_final: 0.8932 (ttmm) REVERT: E 65 ASN cc_start: 0.9086 (p0) cc_final: 0.8579 (p0) REVERT: E 111 MET cc_start: 0.8138 (ppp) cc_final: 0.7883 (ppp) REVERT: E 129 ASP cc_start: 0.8987 (t70) cc_final: 0.8690 (t0) REVERT: E 132 SER cc_start: 0.9435 (m) cc_final: 0.9143 (p) REVERT: E 169 ILE cc_start: 0.9695 (pt) cc_final: 0.9319 (pt) REVERT: E 200 TYR cc_start: 0.8843 (m-80) cc_final: 0.7910 (m-80) REVERT: E 208 TYR cc_start: 0.8818 (m-10) cc_final: 0.8076 (m-10) REVERT: E 229 ASP cc_start: 0.8798 (p0) cc_final: 0.8593 (p0) REVERT: E 251 MET cc_start: 0.8199 (mmt) cc_final: 0.7975 (mmt) REVERT: E 257 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8795 (tm-30) REVERT: E 261 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8108 (tm-30) REVERT: E 262 ASN cc_start: 0.9353 (m-40) cc_final: 0.8808 (m-40) REVERT: E 268 TYR cc_start: 0.8013 (t80) cc_final: 0.7732 (t80) REVERT: E 273 MET cc_start: 0.8394 (ttm) cc_final: 0.8179 (ttm) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.2192 time to fit residues: 129.9357 Evaluate side-chains 327 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13085 Z= 0.373 Angle : 0.913 13.685 17760 Z= 0.465 Chirality : 0.050 0.267 2005 Planarity : 0.006 0.130 2315 Dihedral : 6.579 79.012 1795 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.20), residues: 1625 helix: -0.12 (0.17), residues: 905 sheet: -1.54 (0.40), residues: 165 loop : -2.38 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 18 HIS 0.010 0.001 HIS B 157 PHE 0.033 0.003 PHE D 306 TYR 0.023 0.002 TYR D 110 ARG 0.018 0.001 ARG D 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 1.552 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: A 46 ASN cc_start: 0.9221 (t0) cc_final: 0.8836 (t0) REVERT: A 64 ASN cc_start: 0.9235 (m-40) cc_final: 0.8990 (m-40) REVERT: A 65 ASN cc_start: 0.9209 (p0) cc_final: 0.8862 (p0) REVERT: A 107 MET cc_start: 0.9146 (tmm) cc_final: 0.8743 (tmm) REVERT: A 169 ILE cc_start: 0.9737 (pt) cc_final: 0.9467 (pt) REVERT: A 178 ASP cc_start: 0.8592 (t70) cc_final: 0.8198 (t70) REVERT: A 273 MET cc_start: 0.8756 (mtp) cc_final: 0.8016 (mtp) REVERT: A 282 PHE cc_start: 0.8800 (m-80) cc_final: 0.8594 (m-80) REVERT: B 41 CYS cc_start: 0.7620 (m) cc_final: 0.7276 (m) REVERT: B 46 ASN cc_start: 0.9195 (t0) cc_final: 0.8879 (t0) REVERT: B 92 CYS cc_start: 0.8244 (t) cc_final: 0.7980 (m) REVERT: B 107 MET cc_start: 0.8944 (tmm) cc_final: 0.8663 (tmm) REVERT: B 160 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8850 (mt-10) REVERT: B 192 LYS cc_start: 0.9314 (ttmm) cc_final: 0.8939 (tttm) REVERT: B 197 MET cc_start: 0.9203 (ttm) cc_final: 0.8439 (ttm) REVERT: B 232 ASP cc_start: 0.8479 (m-30) cc_final: 0.8174 (t0) REVERT: B 251 MET cc_start: 0.7969 (mmt) cc_final: 0.7767 (mmt) REVERT: B 268 TYR cc_start: 0.9064 (t80) cc_final: 0.8840 (t80) REVERT: B 282 PHE cc_start: 0.8765 (m-80) cc_final: 0.8431 (m-10) REVERT: C 18 TRP cc_start: 0.8754 (m100) cc_final: 0.8281 (m100) REVERT: C 46 ASN cc_start: 0.9144 (t0) cc_final: 0.8838 (t0) REVERT: C 68 ASP cc_start: 0.8308 (t70) cc_final: 0.7842 (t0) REVERT: C 121 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8206 (tm-30) REVERT: C 163 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8924 (mm-30) REVERT: C 200 TYR cc_start: 0.8814 (m-80) cc_final: 0.8266 (m-80) REVERT: C 227 MET cc_start: 0.9136 (tpp) cc_final: 0.8831 (mmm) REVERT: C 229 ASP cc_start: 0.9150 (p0) cc_final: 0.8912 (p0) REVERT: C 232 ASP cc_start: 0.8475 (m-30) cc_final: 0.8243 (m-30) REVERT: C 259 MET cc_start: 0.9228 (mmt) cc_final: 0.8974 (mmp) REVERT: C 268 TYR cc_start: 0.9084 (t80) cc_final: 0.8862 (t80) REVERT: C 270 MET cc_start: 0.8884 (ttt) cc_final: 0.8527 (mtp) REVERT: C 326 TRP cc_start: 0.8015 (m100) cc_final: 0.6281 (m100) REVERT: D 1 MET cc_start: 0.7640 (ppp) cc_final: 0.7323 (ppp) REVERT: D 18 TRP cc_start: 0.8702 (m100) cc_final: 0.8462 (m100) REVERT: D 46 ASN cc_start: 0.9366 (t0) cc_final: 0.9150 (t0) REVERT: D 78 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.8260 (ttp-110) REVERT: D 92 CYS cc_start: 0.8404 (t) cc_final: 0.8150 (t) REVERT: D 111 MET cc_start: 0.8327 (ttp) cc_final: 0.7140 (tmm) REVERT: D 169 ILE cc_start: 0.9615 (pt) cc_final: 0.9363 (pt) REVERT: D 178 ASP cc_start: 0.8373 (t70) cc_final: 0.8171 (t70) REVERT: D 189 LEU cc_start: 0.9332 (pp) cc_final: 0.8811 (tt) REVERT: D 194 LEU cc_start: 0.9714 (tp) cc_final: 0.9183 (tp) REVERT: D 197 MET cc_start: 0.8306 (tpp) cc_final: 0.7903 (tpp) REVERT: D 200 TYR cc_start: 0.8245 (m-80) cc_final: 0.7115 (m-80) REVERT: D 201 MET cc_start: 0.8157 (mmm) cc_final: 0.7596 (mmm) REVERT: D 227 MET cc_start: 0.8130 (tpt) cc_final: 0.7904 (tpt) REVERT: D 239 ASP cc_start: 0.9038 (t0) cc_final: 0.8785 (t70) REVERT: D 244 CYS cc_start: 0.8968 (m) cc_final: 0.8375 (t) REVERT: D 278 LEU cc_start: 0.9259 (tt) cc_final: 0.8733 (tt) REVERT: D 282 PHE cc_start: 0.8693 (m-80) cc_final: 0.8429 (m-80) REVERT: D 287 PHE cc_start: 0.8093 (m-10) cc_final: 0.7876 (m-10) REVERT: D 305 ILE cc_start: 0.8924 (mt) cc_final: 0.8672 (mm) REVERT: E 5 LYS cc_start: 0.9251 (ttmm) cc_final: 0.8950 (ttmm) REVERT: E 65 ASN cc_start: 0.9113 (p0) cc_final: 0.8622 (p0) REVERT: E 111 MET cc_start: 0.8187 (ppp) cc_final: 0.7911 (ppp) REVERT: E 129 ASP cc_start: 0.9031 (t70) cc_final: 0.8759 (t0) REVERT: E 132 SER cc_start: 0.9473 (m) cc_final: 0.9176 (p) REVERT: E 169 ILE cc_start: 0.9633 (pt) cc_final: 0.9237 (pt) REVERT: E 208 TYR cc_start: 0.8857 (m-10) cc_final: 0.8591 (m-10) REVERT: E 229 ASP cc_start: 0.8825 (p0) cc_final: 0.8567 (p0) REVERT: E 251 MET cc_start: 0.8177 (mmt) cc_final: 0.7944 (mmt) REVERT: E 257 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8837 (tm-30) REVERT: E 261 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8137 (tm-30) REVERT: E 262 ASN cc_start: 0.9326 (m-40) cc_final: 0.8728 (m-40) REVERT: E 268 TYR cc_start: 0.8233 (t80) cc_final: 0.7715 (t80) REVERT: E 273 MET cc_start: 0.8640 (ttm) cc_final: 0.8359 (ttm) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.2168 time to fit residues: 123.7719 Evaluate side-chains 309 residues out of total 1385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 0.0170 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.071844 restraints weight = 47064.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073941 restraints weight = 29033.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.075412 restraints weight = 20417.604| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13085 Z= 0.245 Angle : 0.885 12.143 17760 Z= 0.433 Chirality : 0.048 0.247 2005 Planarity : 0.006 0.114 2315 Dihedral : 6.467 78.626 1795 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.49 (0.20), residues: 1625 helix: -0.01 (0.17), residues: 895 sheet: -1.22 (0.44), residues: 140 loop : -2.42 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP B 146 HIS 0.008 0.001 HIS B 157 PHE 0.045 0.003 PHE C 306 TYR 0.017 0.002 TYR A 110 ARG 0.016 0.001 ARG D 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.55 seconds wall clock time: 54 minutes 13.84 seconds (3253.84 seconds total)