Starting phenix.real_space_refine on Fri Nov 15 02:18:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsj_60417/11_2024/8zsj_60417.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsj_60417/11_2024/8zsj_60417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsj_60417/11_2024/8zsj_60417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsj_60417/11_2024/8zsj_60417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsj_60417/11_2024/8zsj_60417.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zsj_60417/11_2024/8zsj_60417.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 60 5.16 5 C 5166 2.51 5 N 1390 2.21 5 O 1502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8118 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1889 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2200 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 5.41, per 1000 atoms: 0.67 Number of scatterers: 8118 At special positions: 0 Unit cell: (80.704, 99.008, 133.952, 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 60 16.00 O 1502 8.00 N 1390 7.00 C 5166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.557A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.680A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.245A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.756A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.658A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 23 through 52 removed outlier: 3.667A pdb=" N SER R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 29 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS R 52 " --> pdb=" O ILE R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 86 Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 92 through 127 Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 179 removed outlier: 3.777A pdb=" N TYR R 173 " --> pdb=" O GLU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 230 removed outlier: 3.549A pdb=" N ILE R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 274 removed outlier: 3.631A pdb=" N LYS R 251 " --> pdb=" O ARG R 247 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.522A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP R 291 " --> pdb=" O ASP R 287 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75 removed outlier: 6.446A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL A 86 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 45 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N ALA A 105 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG A 42 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 107 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 44 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 109 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 46 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASP A 111 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.520A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.513A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.416A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.514A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.697A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.578A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.401A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.976A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1314 1.31 - 1.43: 2289 1.43 - 1.56: 4604 1.56 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 8294 Sorted by residual: bond pdb=" C CYS B 294 " pdb=" O CYS B 294 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.28e-02 6.10e+03 1.94e+01 bond pdb=" CA LEU B 308 " pdb=" C LEU B 308 " ideal model delta sigma weight residual 1.528 1.485 0.043 1.04e-02 9.25e+03 1.72e+01 bond pdb=" C LEU B 210 " pdb=" O LEU B 210 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.22e-02 6.72e+03 1.52e+01 bond pdb=" CA LEU B 210 " pdb=" C LEU B 210 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.23e-02 6.61e+03 1.29e+01 bond pdb=" CA GLU A 92 " pdb=" CB GLU A 92 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.35e-02 5.49e+03 1.16e+01 ... (remaining 8289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 10983 2.08 - 4.17: 242 4.17 - 6.25: 21 6.25 - 8.34: 2 8.34 - 10.42: 3 Bond angle restraints: 11251 Sorted by residual: angle pdb=" N PHE A 70 " pdb=" CA PHE A 70 " pdb=" C PHE A 70 " ideal model delta sigma weight residual 110.30 100.05 10.25 1.50e+00 4.44e-01 4.67e+01 angle pdb=" C PHE A 70 " pdb=" CA PHE A 70 " pdb=" CB PHE A 70 " ideal model delta sigma weight residual 110.06 118.15 -8.09 1.39e+00 5.18e-01 3.39e+01 angle pdb=" N VAL A 57 " pdb=" CA VAL A 57 " pdb=" C VAL A 57 " ideal model delta sigma weight residual 112.17 107.42 4.75 9.50e-01 1.11e+00 2.50e+01 angle pdb=" N GLU R 170 " pdb=" CA GLU R 170 " pdb=" C GLU R 170 " ideal model delta sigma weight residual 111.71 106.56 5.15 1.15e+00 7.56e-01 2.01e+01 angle pdb=" N GLY R 167 " pdb=" CA GLY R 167 " pdb=" C GLY R 167 " ideal model delta sigma weight residual 115.64 109.53 6.11 1.46e+00 4.69e-01 1.75e+01 ... (remaining 11246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4484 16.07 - 32.13: 371 32.13 - 48.20: 85 48.20 - 64.27: 15 64.27 - 80.34: 8 Dihedral angle restraints: 4963 sinusoidal: 1949 harmonic: 3014 Sorted by residual: dihedral pdb=" CA HIS R 50 " pdb=" C HIS R 50 " pdb=" N PHE R 51 " pdb=" CA PHE R 51 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.06 39.94 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CG ARG N 67 " pdb=" CD ARG N 67 " pdb=" NE ARG N 67 " pdb=" CZ ARG N 67 " ideal model delta sinusoidal sigma weight residual 90.00 131.74 -41.74 2 1.50e+01 4.44e-03 9.45e+00 ... (remaining 4960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1063 0.067 - 0.133: 178 0.133 - 0.200: 21 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CA THR N 91 " pdb=" N THR N 91 " pdb=" C THR N 91 " pdb=" CB THR N 91 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ASP R 287 " pdb=" N ASP R 287 " pdb=" C ASP R 287 " pdb=" CB ASP R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA VAL A 57 " pdb=" N VAL A 57 " pdb=" C VAL A 57 " pdb=" CB VAL A 57 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1263 not shown) Planarity restraints: 1429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 83 " 0.418 9.50e-02 1.11e+02 1.88e-01 2.15e+01 pdb=" NE ARG R 83 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG R 83 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG R 83 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 83 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 308 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO R 309 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO R 309 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 309 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 312 " 0.383 9.50e-02 1.11e+02 1.72e-01 1.80e+01 pdb=" NE ARG R 312 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG R 312 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG R 312 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 312 " 0.013 2.00e-02 2.50e+03 ... (remaining 1426 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1105 2.75 - 3.29: 7970 3.29 - 3.83: 14027 3.83 - 4.36: 17110 4.36 - 4.90: 29488 Nonbonded interactions: 69700 Sorted by model distance: nonbonded pdb=" OG SER N 7 " pdb=" OG SER N 21 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR R 56 " pdb=" OD1 ASN R 59 " model vdw 2.253 3.040 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP R 103 " pdb=" O HOH R 501 " model vdw 2.273 3.040 ... (remaining 69695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.870 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.005 0.056 8294 Z= 0.324 Angle : 0.684 10.422 11251 Z= 0.444 Chirality : 0.051 0.333 1266 Planarity : 0.011 0.188 1429 Dihedral : 12.911 80.336 3006 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.12 % Allowed : 1.16 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 1021 helix: 2.24 (0.25), residues: 387 sheet: -0.06 (0.35), residues: 215 loop : -0.62 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 291 HIS 0.004 0.001 HIS R 63 PHE 0.018 0.001 PHE R 91 TYR 0.010 0.001 TYR R 308 ARG 0.016 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7879 (m-30) cc_final: 0.7586 (m-30) REVERT: N 53 GLN cc_start: 0.8750 (mp10) cc_final: 0.8533 (mp10) REVERT: R 95 PHE cc_start: 0.7456 (t80) cc_final: 0.7231 (t80) REVERT: R 302 MET cc_start: 0.7989 (mtt) cc_final: 0.7758 (mtp) outliers start: 1 outliers final: 1 residues processed: 178 average time/residue: 1.4136 time to fit residues: 265.2103 Evaluate side-chains 142 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 184 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 17 GLN B 44 GLN B 237 ASN B 239 ASN B 259 GLN B 340 ASN N 3 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8294 Z= 0.227 Angle : 0.546 10.230 11251 Z= 0.291 Chirality : 0.042 0.159 1266 Planarity : 0.005 0.073 1429 Dihedral : 4.318 27.525 1191 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.73 % Allowed : 11.45 % Favored : 86.82 % 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: 1.05 (0.27), residues: 1021 helix: 2.40 (0.25), residues: 389 sheet: -0.01 (0.35), residues: 212 loop : -0.54 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS R 63 PHE 0.013 0.001 PHE R 51 TYR 0.012 0.001 TYR A 115 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7823 (m-30) cc_final: 0.7566 (m-30) REVERT: B 59 TYR cc_start: 0.8222 (m-80) cc_final: 0.7936 (m-80) REVERT: B 75 GLN cc_start: 0.7490 (tt0) cc_final: 0.7277 (tt0) REVERT: B 134 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6488 (ptm160) REVERT: R 262 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8166 (mp) REVERT: R 302 MET cc_start: 0.7945 (mtt) cc_final: 0.7665 (mtp) outliers start: 15 outliers final: 4 residues processed: 154 average time/residue: 1.4162 time to fit residues: 230.3888 Evaluate side-chains 145 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 17 GLN B 44 GLN B 75 GLN B 237 ASN B 259 GLN N 39 GLN N 77 ASN R 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8294 Z= 0.234 Angle : 0.536 10.008 11251 Z= 0.285 Chirality : 0.042 0.147 1266 Planarity : 0.005 0.061 1429 Dihedral : 4.336 30.070 1191 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.31 % Allowed : 14.34 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1021 helix: 2.31 (0.25), residues: 397 sheet: -0.09 (0.33), residues: 217 loop : -0.44 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 214 PHE 0.017 0.001 PHE R 91 TYR 0.017 0.001 TYR N 60 ARG 0.006 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7861 (m-30) cc_final: 0.7594 (m-30) REVERT: B 134 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6510 (ptm160) REVERT: B 325 MET cc_start: 0.7919 (tpp) cc_final: 0.7648 (mmm) REVERT: R 262 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8149 (mp) REVERT: R 302 MET cc_start: 0.7945 (mtt) cc_final: 0.7667 (mtp) outliers start: 20 outliers final: 6 residues processed: 156 average time/residue: 1.3755 time to fit residues: 226.3583 Evaluate side-chains 146 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 237 ASN B 259 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8294 Z= 0.218 Angle : 0.528 9.891 11251 Z= 0.278 Chirality : 0.041 0.146 1266 Planarity : 0.004 0.056 1429 Dihedral : 4.284 30.395 1191 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.54 % Allowed : 15.84 % Favored : 81.62 % 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: 1.06 (0.26), residues: 1021 helix: 2.32 (0.25), residues: 397 sheet: -0.07 (0.33), residues: 217 loop : -0.43 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 214 PHE 0.026 0.001 PHE R 91 TYR 0.021 0.001 TYR N 60 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6482 (ptm160) REVERT: B 325 MET cc_start: 0.7890 (tpp) cc_final: 0.7629 (mmm) REVERT: R 262 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8180 (mp) REVERT: R 302 MET cc_start: 0.7949 (mtt) cc_final: 0.7664 (mtp) outliers start: 22 outliers final: 5 residues processed: 156 average time/residue: 1.2153 time to fit residues: 201.5289 Evaluate side-chains 142 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 131 ASN B 17 GLN B 44 GLN B 237 ASN B 259 GLN N 77 ASN R 53 GLN R 55 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8294 Z= 0.257 Angle : 0.545 9.411 11251 Z= 0.288 Chirality : 0.042 0.146 1266 Planarity : 0.004 0.053 1429 Dihedral : 4.225 18.837 1190 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.43 % Allowed : 16.42 % Favored : 81.16 % 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: 1.05 (0.26), residues: 1021 helix: 2.33 (0.25), residues: 398 sheet: -0.13 (0.32), residues: 217 loop : -0.43 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS R 63 PHE 0.017 0.001 PHE R 91 TYR 0.023 0.002 TYR N 60 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8028 (ttt180) REVERT: B 134 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6490 (ptm160) REVERT: B 325 MET cc_start: 0.7888 (tpp) cc_final: 0.7632 (mmm) REVERT: R 262 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8316 (mp) REVERT: R 302 MET cc_start: 0.7952 (mtt) cc_final: 0.7665 (mtp) outliers start: 21 outliers final: 10 residues processed: 152 average time/residue: 1.2443 time to fit residues: 200.6477 Evaluate side-chains 149 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 75 GLN B 237 ASN B 259 GLN N 31 ASN N 77 ASN R 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8294 Z= 0.205 Angle : 0.528 9.460 11251 Z= 0.279 Chirality : 0.041 0.142 1266 Planarity : 0.004 0.051 1429 Dihedral : 4.143 18.283 1190 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.43 % Allowed : 18.15 % Favored : 79.42 % 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: 1.06 (0.26), residues: 1021 helix: 2.36 (0.25), residues: 400 sheet: -0.18 (0.32), residues: 221 loop : -0.45 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 63 PHE 0.015 0.001 PHE R 91 TYR 0.026 0.001 TYR N 60 ARG 0.006 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8013 (ttt180) REVERT: B 134 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6489 (ptm160) REVERT: B 325 MET cc_start: 0.7901 (tpp) cc_final: 0.7621 (mmm) REVERT: R 262 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8164 (mp) REVERT: R 302 MET cc_start: 0.7950 (mtt) cc_final: 0.7654 (mtp) outliers start: 21 outliers final: 10 residues processed: 150 average time/residue: 1.2044 time to fit residues: 192.2207 Evaluate side-chains 148 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 0.0570 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 237 ASN B 259 GLN N 39 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8294 Z= 0.195 Angle : 0.529 9.345 11251 Z= 0.279 Chirality : 0.041 0.141 1266 Planarity : 0.004 0.051 1429 Dihedral : 4.090 17.873 1190 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.20 % Allowed : 18.96 % Favored : 78.84 % 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: 1.07 (0.26), residues: 1021 helix: 2.38 (0.25), residues: 400 sheet: -0.08 (0.32), residues: 216 loop : -0.52 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 63 PHE 0.011 0.001 PHE A 74 TYR 0.015 0.001 TYR N 60 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6474 (ptm160) REVERT: B 325 MET cc_start: 0.7899 (tpp) cc_final: 0.7627 (mmm) REVERT: N 43 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7966 (mtpp) REVERT: R 262 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8169 (mp) REVERT: R 302 MET cc_start: 0.7943 (mtt) cc_final: 0.7645 (mtp) outliers start: 19 outliers final: 10 residues processed: 151 average time/residue: 1.2204 time to fit residues: 195.9626 Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 88 ASN B 237 ASN B 259 GLN N 39 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8294 Z= 0.225 Angle : 0.546 9.339 11251 Z= 0.288 Chirality : 0.041 0.140 1266 Planarity : 0.004 0.050 1429 Dihedral : 4.121 17.686 1190 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.31 % Allowed : 19.65 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1021 helix: 2.34 (0.25), residues: 399 sheet: -0.12 (0.32), residues: 217 loop : -0.52 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS R 63 PHE 0.016 0.001 PHE R 91 TYR 0.015 0.002 TYR N 60 ARG 0.008 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6461 (ptm160) REVERT: B 325 MET cc_start: 0.7895 (tpp) cc_final: 0.7675 (mmm) REVERT: N 43 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7985 (mtpp) REVERT: R 262 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8332 (mp) REVERT: R 302 MET cc_start: 0.7957 (mtt) cc_final: 0.7667 (mtp) outliers start: 20 outliers final: 9 residues processed: 144 average time/residue: 1.2166 time to fit residues: 186.0506 Evaluate side-chains 143 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 0.0060 chunk 54 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 259 GLN G 18 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8294 Z= 0.177 Angle : 0.538 9.010 11251 Z= 0.283 Chirality : 0.040 0.147 1266 Planarity : 0.004 0.050 1429 Dihedral : 4.036 17.610 1190 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.85 % Allowed : 20.12 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1021 helix: 2.48 (0.25), residues: 393 sheet: 0.01 (0.32), residues: 214 loop : -0.55 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.002 0.001 HIS R 63 PHE 0.011 0.001 PHE A 74 TYR 0.025 0.001 TYR N 60 ARG 0.014 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6425 (ptm160) REVERT: B 325 MET cc_start: 0.7891 (tpp) cc_final: 0.7628 (mmm) REVERT: N 43 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7922 (mtpp) REVERT: R 207 LEU cc_start: 0.7568 (mt) cc_final: 0.7318 (tp) REVERT: R 262 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8165 (mp) REVERT: R 302 MET cc_start: 0.7936 (mtt) cc_final: 0.7627 (mtp) outliers start: 16 outliers final: 7 residues processed: 152 average time/residue: 1.2119 time to fit residues: 195.7618 Evaluate side-chains 144 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 259 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8294 Z= 0.184 Angle : 0.537 9.038 11251 Z= 0.283 Chirality : 0.040 0.144 1266 Planarity : 0.005 0.067 1429 Dihedral : 3.982 17.558 1190 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.27 % Allowed : 21.27 % Favored : 77.46 % 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: 1.08 (0.26), residues: 1021 helix: 2.46 (0.25), residues: 392 sheet: 0.10 (0.33), residues: 208 loop : -0.65 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 63 PHE 0.020 0.001 PHE R 91 TYR 0.025 0.001 TYR N 60 ARG 0.016 0.001 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: B 134 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6403 (ptm160) REVERT: B 217 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7202 (ppp) REVERT: B 325 MET cc_start: 0.7913 (tpp) cc_final: 0.7652 (mmm) REVERT: N 43 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7918 (mtpp) REVERT: R 262 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8191 (mp) REVERT: R 302 MET cc_start: 0.7942 (mtt) cc_final: 0.7661 (mtp) outliers start: 11 outliers final: 6 residues processed: 145 average time/residue: 1.1854 time to fit residues: 183.0317 Evaluate side-chains 140 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS B 17 GLN B 259 GLN N 77 ASN R 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.149377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114205 restraints weight = 10381.730| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.52 r_work: 0.3269 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8294 Z= 0.264 Angle : 0.571 9.304 11251 Z= 0.301 Chirality : 0.042 0.143 1266 Planarity : 0.005 0.061 1429 Dihedral : 4.139 18.033 1190 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.27 % Allowed : 21.85 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1021 helix: 2.36 (0.25), residues: 399 sheet: -0.02 (0.32), residues: 216 loop : -0.61 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 211 HIS 0.005 0.001 HIS R 63 PHE 0.010 0.001 PHE A 74 TYR 0.025 0.002 TYR N 60 ARG 0.015 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3846.22 seconds wall clock time: 69 minutes 19.10 seconds (4159.10 seconds total)