Starting phenix.real_space_refine on Fri Jul 19 07:17:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/07_2024/7t2g_25612.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/07_2024/7t2g_25612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/07_2024/7t2g_25612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/07_2024/7t2g_25612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/07_2024/7t2g_25612.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/07_2024/7t2g_25612.cif" } resolution = 2.5 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= 0.028 sd= 0.242 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 59 5.16 5 C 4461 2.51 5 N 1154 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6922 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1690 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2481 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 348 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2279 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 288, 2270 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 288, 2270 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2317 Chain: "R" Number of atoms: 124 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 11, 94 Unusual residues: {'CLR': 2, 'EIG': 1} Classifications: {'undetermined': 3, 'water': 8} Link IDs: {None: 10} Conformer: "B" Number of residues, atoms: 11, 94 Unusual residues: {'CLR': 2, 'EIG': 1} Classifications: {'undetermined': 3, 'water': 8} Link IDs: {None: 10} bond proxies already assigned to first conformer: 62 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01AEIG R 501 " occ=0.50 ... (58 atoms not shown) pdb=" O05BEIG R 501 " occ=0.50 Time building chain proxies: 5.48, per 1000 atoms: 0.79 Number of scatterers: 6922 At special positions: 0 Unit cell: (91.84, 98.4, 114.8, 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 59 16.00 O 1248 8.00 N 1154 7.00 C 4461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.6 seconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 47.8% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.630A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.061A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.722A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.691A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 46 removed outlier: 4.638A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 Processing helix chain 'R' and resid 101 through 120 removed outlier: 3.630A pdb=" N THR R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 130 Processing helix chain 'R' and resid 135 through 171 removed outlier: 4.173A pdb=" N LEU R 139 " --> pdb=" O PHE R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 179 removed outlier: 4.142A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 195 Processing helix chain 'R' and resid 195 through 206 Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 224 through 241 removed outlier: 3.598A pdb=" N TRP R 228 " --> pdb=" O PRO R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 260 Processing helix chain 'R' and resid 268 through 306 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 311 through 337 removed outlier: 3.852A pdb=" N VAL R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN R 328 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 340 through 348 removed outlier: 3.610A pdb=" N ARG R 345 " --> pdb=" O GLU R 341 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS R 346 " --> pdb=" O ASN R 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.189A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.524A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.826A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.680A 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: 3.987A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.980A 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: 6.524A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.022A 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: 6.696A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.172A 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: 3.526A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.690A 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: 5.826A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 208 through 211 398 hydrogen bonds defined for protein. 1158 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: 2.04 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1094 1.30 - 1.43: 1855 1.43 - 1.56: 4029 1.56 - 1.69: 6 1.69 - 1.82: 83 Bond restraints: 7067 Sorted by residual: bond pdb=" C08BEIG R 501 " pdb=" N01BEIG R 501 " ideal model delta sigma weight residual 1.448 1.271 0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C17BEIG R 501 " pdb=" C19BEIG R 501 " ideal model delta sigma weight residual 1.470 1.611 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C08BEIG R 501 " pdb=" C09BEIG R 501 " ideal model delta sigma weight residual 1.529 1.404 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C LEU B 252 " pdb=" O LEU B 252 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.22e-02 6.72e+03 2.97e+01 bond pdb=" C17AEIG R 501 " pdb=" C20AEIG R 501 " ideal model delta sigma weight residual 1.348 1.445 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 7062 not shown) Histogram of bond angle deviations from ideal: 94.75 - 103.13: 54 103.13 - 111.51: 3257 111.51 - 119.88: 3032 119.88 - 128.26: 3220 128.26 - 136.63: 69 Bond angle restraints: 9632 Sorted by residual: angle pdb=" C09BEIG R 501 " pdb=" C08BEIG R 501 " pdb=" C12BEIG R 501 " ideal model delta sigma weight residual 114.95 94.75 20.20 3.00e+00 1.11e-01 4.53e+01 angle pdb=" N GLY B 64 " pdb=" CA GLY B 64 " pdb=" C GLY B 64 " ideal model delta sigma weight residual 112.82 105.38 7.44 1.38e+00 5.25e-01 2.90e+01 angle pdb=" N ASN R 328 " pdb=" CA ASN R 328 " pdb=" C ASN R 328 " ideal model delta sigma weight residual 112.54 106.25 6.29 1.22e+00 6.72e-01 2.66e+01 angle pdb=" N SER R 329 " pdb=" CA SER R 329 " pdb=" C SER R 329 " ideal model delta sigma weight residual 112.23 105.84 6.39 1.26e+00 6.30e-01 2.57e+01 angle pdb=" N LYS C 32 " pdb=" CA LYS C 32 " pdb=" C LYS C 32 " ideal model delta sigma weight residual 112.90 106.27 6.63 1.31e+00 5.83e-01 2.56e+01 ... (remaining 9627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 4044 17.02 - 34.03: 238 34.03 - 51.05: 35 51.05 - 68.07: 18 68.07 - 85.09: 4 Dihedral angle restraints: 4339 sinusoidal: 1710 harmonic: 2629 Sorted by residual: dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASN B 293 " pdb=" C ASN B 293 " pdb=" N CYS B 294 " pdb=" CA CYS B 294 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1069 0.096 - 0.192: 68 0.192 - 0.288: 1 0.288 - 0.383: 1 0.383 - 0.479: 1 Chirality restraints: 1140 Sorted by residual: chirality pdb=" C08BEIG R 501 " pdb=" C09BEIG R 501 " pdb=" C10BEIG R 501 " pdb=" C12BEIG R 501 " both_signs ideal model delta sigma weight residual False -2.77 -2.29 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C14BEIG R 501 " pdb=" C13BEIG R 501 " pdb=" C15BEIG R 501 " pdb=" C17BEIG R 501 " both_signs ideal model delta sigma weight residual False -2.26 -2.58 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C10AEIG R 501 " pdb=" C08AEIG R 501 " pdb=" C13AEIG R 501 " pdb=" N02AEIG R 501 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1137 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14BEIG R 501 " -0.022 2.00e-02 2.50e+03 4.86e-02 2.95e+01 pdb=" C17BEIG R 501 " 0.016 2.00e-02 2.50e+03 pdb=" C19BEIG R 501 " 0.029 2.00e-02 2.50e+03 pdb=" C20BEIG R 501 " -0.082 2.00e-02 2.50e+03 pdb=" O03BEIG R 501 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 251 " 0.413 9.50e-02 1.11e+02 1.85e-01 2.10e+01 pdb=" NE ARG B 251 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG B 251 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 251 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 251 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 252 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C LEU B 252 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU B 252 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE B 253 " -0.024 2.00e-02 2.50e+03 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1007 2.75 - 3.29: 7286 3.29 - 3.83: 12842 3.83 - 4.36: 16022 4.36 - 4.90: 25912 Nonbonded interactions: 63069 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASN B 110 " pdb=" NZ LYS B 127 " model vdw 2.284 2.520 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.300 2.440 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.308 2.520 nonbonded pdb=" OD2 ASP R 147 " pdb=" OH TYR R 326 " model vdw 2.314 2.440 ... (remaining 63064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.690 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.177 7067 Z= 0.471 Angle : 0.880 20.195 9632 Z= 0.534 Chirality : 0.049 0.479 1140 Planarity : 0.008 0.185 1190 Dihedral : 12.032 85.085 2630 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.00 % Allowed : 7.30 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.28), residues: 890 helix: 1.29 (0.27), residues: 376 sheet: 0.19 (0.37), residues: 175 loop : -0.38 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 192 HIS 0.010 0.001 HIS B 225 PHE 0.015 0.002 PHE B 151 TYR 0.019 0.002 TYR R 326 ARG 0.005 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 0.738 Fit side-chains REVERT: B 75 GLN cc_start: 0.7678 (mm110) cc_final: 0.7038 (mm110) REVERT: B 83 ASP cc_start: 0.8110 (t0) cc_final: 0.7830 (t0) outliers start: 7 outliers final: 2 residues processed: 168 average time/residue: 1.1179 time to fit residues: 198.1176 Evaluate side-chains 154 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain R residue 160 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 269 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 259 GLN B 293 ASN B 340 ASN R 109 ASN R 150 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7067 Z= 0.300 Angle : 0.611 5.761 9632 Z= 0.328 Chirality : 0.044 0.152 1140 Planarity : 0.004 0.037 1190 Dihedral : 6.726 61.306 1208 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.86 % Allowed : 12.16 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.76 (0.28), residues: 890 helix: 1.72 (0.25), residues: 389 sheet: 0.19 (0.38), residues: 168 loop : -0.74 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS B 54 PHE 0.018 0.002 PHE B 151 TYR 0.014 0.002 TYR R 326 ARG 0.004 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 0.762 Fit side-chains REVERT: A 285 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7182 (mt) REVERT: B 32 GLN cc_start: 0.7590 (mt0) cc_final: 0.7374 (mt0) REVERT: B 75 GLN cc_start: 0.7730 (mm110) cc_final: 0.6982 (mm110) REVERT: B 83 ASP cc_start: 0.8111 (t0) cc_final: 0.7904 (t0) REVERT: R 230 ASN cc_start: 0.7785 (m-40) cc_final: 0.7516 (m-40) REVERT: R 280 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7462 (mtt-85) outliers start: 20 outliers final: 7 residues processed: 165 average time/residue: 1.1423 time to fit residues: 198.5632 Evaluate side-chains 160 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 255 MET Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 280 ARG Chi-restraints excluded: chain R residue 316 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS A 269 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN R 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7067 Z= 0.208 Angle : 0.522 5.537 9632 Z= 0.281 Chirality : 0.041 0.151 1140 Planarity : 0.004 0.039 1190 Dihedral : 5.927 55.431 1206 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.58 % Allowed : 13.73 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.79 (0.28), residues: 890 helix: 1.83 (0.26), residues: 398 sheet: -0.03 (0.37), residues: 172 loop : -0.79 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE R 237 TYR 0.009 0.001 TYR R 149 ARG 0.005 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 0.794 Fit side-chains REVERT: A 207 GLU cc_start: 0.7113 (tp30) cc_final: 0.6756 (mm-30) REVERT: A 285 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7164 (mt) REVERT: A 308 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6779 (mm-30) REVERT: B 75 GLN cc_start: 0.7694 (mm110) cc_final: 0.6799 (mm-40) outliers start: 18 outliers final: 2 residues processed: 170 average time/residue: 1.1525 time to fit residues: 206.3808 Evaluate side-chains 152 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 160 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS A 269 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7067 Z= 0.224 Angle : 0.533 5.488 9632 Z= 0.284 Chirality : 0.041 0.162 1140 Planarity : 0.003 0.037 1190 Dihedral : 5.757 55.331 1206 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.72 % Allowed : 14.88 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.77 (0.28), residues: 890 helix: 1.81 (0.25), residues: 398 sheet: 0.02 (0.37), residues: 173 loop : -0.83 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.013 0.002 PHE R 237 TYR 0.010 0.001 TYR R 326 ARG 0.006 0.000 ARG R 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 0.692 Fit side-chains REVERT: A 19 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7159 (pt) REVERT: A 207 GLU cc_start: 0.7238 (tp30) cc_final: 0.6862 (mm-30) REVERT: A 285 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7143 (mt) REVERT: A 308 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6821 (mm-30) REVERT: B 44 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: B 75 GLN cc_start: 0.7743 (mm110) cc_final: 0.6825 (mm-40) outliers start: 19 outliers final: 6 residues processed: 160 average time/residue: 1.1661 time to fit residues: 196.3717 Evaluate side-chains 159 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0000 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS A 269 ASN A 311 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7067 Z= 0.231 Angle : 0.542 5.556 9632 Z= 0.289 Chirality : 0.041 0.154 1140 Planarity : 0.004 0.035 1190 Dihedral : 5.712 55.861 1206 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.15 % Allowed : 15.31 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.72 (0.27), residues: 890 helix: 1.75 (0.25), residues: 399 sheet: -0.01 (0.37), residues: 173 loop : -0.85 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.013 0.002 PHE R 237 TYR 0.010 0.001 TYR R 326 ARG 0.007 0.000 ARG R 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 0.711 Fit side-chains REVERT: A 19 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7172 (pt) REVERT: A 207 GLU cc_start: 0.7109 (tp30) cc_final: 0.6818 (mm-30) REVERT: A 285 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7134 (mt) REVERT: A 308 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6850 (mm-30) REVERT: B 44 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: B 75 GLN cc_start: 0.7707 (mm110) cc_final: 0.6821 (mm-40) REVERT: B 83 ASP cc_start: 0.8105 (t0) cc_final: 0.7848 (t0) outliers start: 22 outliers final: 9 residues processed: 157 average time/residue: 1.1306 time to fit residues: 187.1972 Evaluate side-chains 158 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS A 269 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7067 Z= 0.220 Angle : 0.541 7.743 9632 Z= 0.286 Chirality : 0.041 0.152 1140 Planarity : 0.004 0.035 1190 Dihedral : 5.535 55.828 1205 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.15 % Allowed : 16.60 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.76 (0.28), residues: 890 helix: 1.81 (0.25), residues: 400 sheet: -0.10 (0.37), residues: 180 loop : -0.80 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.012 0.002 PHE B 199 TYR 0.010 0.001 TYR R 326 ARG 0.006 0.000 ARG R 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.781 Fit side-chains REVERT: A 19 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7178 (pt) REVERT: A 207 GLU cc_start: 0.7228 (tp30) cc_final: 0.6925 (mm-30) REVERT: A 285 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7125 (mt) REVERT: A 308 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6867 (mm-30) REVERT: B 44 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: B 75 GLN cc_start: 0.7715 (mm110) cc_final: 0.6814 (mm-40) REVERT: B 83 ASP cc_start: 0.8119 (t0) cc_final: 0.7841 (t0) outliers start: 22 outliers final: 11 residues processed: 163 average time/residue: 1.1514 time to fit residues: 197.6561 Evaluate side-chains 161 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN R 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7067 Z= 0.203 Angle : 0.529 6.243 9632 Z= 0.282 Chirality : 0.041 0.152 1140 Planarity : 0.003 0.035 1190 Dihedral : 5.362 55.674 1205 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.72 % Allowed : 17.31 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.79 (0.28), residues: 890 helix: 1.81 (0.25), residues: 399 sheet: -0.02 (0.37), residues: 177 loop : -0.80 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR R 149 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7170 (pt) REVERT: A 52 GLN cc_start: 0.7147 (mm-40) cc_final: 0.6885 (mm110) REVERT: A 53 MET cc_start: 0.4781 (mtt) cc_final: 0.3647 (mpp) REVERT: A 207 GLU cc_start: 0.7052 (tp30) cc_final: 0.6822 (mm-30) REVERT: A 285 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7120 (mt) REVERT: A 308 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6861 (mm-30) REVERT: B 44 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: B 75 GLN cc_start: 0.7685 (mm110) cc_final: 0.6742 (mm-40) REVERT: B 83 ASP cc_start: 0.8078 (t0) cc_final: 0.7819 (t0) REVERT: R 276 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.7220 (ttp80) outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 1.1530 time to fit residues: 187.1220 Evaluate side-chains 157 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 273 ARG Chi-restraints excluded: chain R residue 282 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7067 Z= 0.325 Angle : 0.620 6.763 9632 Z= 0.329 Chirality : 0.044 0.177 1140 Planarity : 0.004 0.033 1190 Dihedral : 5.928 57.597 1205 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.29 % Allowed : 17.60 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 890 helix: 1.56 (0.25), residues: 398 sheet: -0.08 (0.37), residues: 179 loop : -0.85 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 192 HIS 0.007 0.002 HIS B 54 PHE 0.015 0.002 PHE B 151 TYR 0.012 0.002 TYR R 326 ARG 0.007 0.001 ARG R 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7216 (pt) REVERT: A 53 MET cc_start: 0.4882 (mtt) cc_final: 0.3709 (mpp) REVERT: A 207 GLU cc_start: 0.7185 (tp30) cc_final: 0.6882 (mm-30) REVERT: A 285 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7124 (mt) REVERT: A 312 LYS cc_start: 0.7335 (mmmt) cc_final: 0.6953 (mmtt) REVERT: B 44 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7155 (mt0) REVERT: B 75 GLN cc_start: 0.7716 (mm110) cc_final: 0.6768 (mm-40) REVERT: B 83 ASP cc_start: 0.8130 (t0) cc_final: 0.7878 (t0) outliers start: 23 outliers final: 11 residues processed: 161 average time/residue: 1.1350 time to fit residues: 192.6986 Evaluate side-chains 161 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 273 ARG Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 316 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7067 Z= 0.212 Angle : 0.545 6.524 9632 Z= 0.290 Chirality : 0.041 0.152 1140 Planarity : 0.003 0.034 1190 Dihedral : 5.490 55.532 1205 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.00 % Allowed : 19.31 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.65 (0.27), residues: 890 helix: 1.66 (0.25), residues: 396 sheet: -0.04 (0.37), residues: 178 loop : -0.81 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.002 PHE B 199 TYR 0.010 0.001 TYR R 128 ARG 0.007 0.000 ARG R 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7175 (pt) REVERT: A 52 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6921 (mm110) REVERT: A 53 MET cc_start: 0.4674 (mtt) cc_final: 0.3762 (mpp) REVERT: A 207 GLU cc_start: 0.7171 (tp30) cc_final: 0.6882 (mm-30) REVERT: A 285 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7120 (mt) REVERT: A 308 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6799 (mm-30) REVERT: A 312 LYS cc_start: 0.7128 (mmmt) cc_final: 0.6840 (mmtt) REVERT: B 44 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: B 75 GLN cc_start: 0.7688 (mm110) cc_final: 0.6672 (mm-40) REVERT: B 83 ASP cc_start: 0.8073 (t0) cc_final: 0.7825 (t0) REVERT: R 276 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7186 (ttp80) outliers start: 14 outliers final: 8 residues processed: 153 average time/residue: 1.2554 time to fit residues: 202.0397 Evaluate side-chains 153 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 273 ARG Chi-restraints excluded: chain R residue 316 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7067 Z= 0.224 Angle : 0.552 6.642 9632 Z= 0.293 Chirality : 0.042 0.155 1140 Planarity : 0.004 0.034 1190 Dihedral : 5.524 56.114 1205 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.29 % Allowed : 19.46 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.68 (0.28), residues: 890 helix: 1.67 (0.25), residues: 398 sheet: -0.10 (0.38), residues: 180 loop : -0.73 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.002 PHE B 199 TYR 0.009 0.001 TYR R 128 ARG 0.007 0.000 ARG R 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7180 (pt) REVERT: A 53 MET cc_start: 0.4631 (mtt) cc_final: 0.3739 (mpp) REVERT: A 207 GLU cc_start: 0.7229 (tp30) cc_final: 0.6916 (mm-30) REVERT: A 285 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7124 (mt) REVERT: A 308 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6798 (mm-30) REVERT: A 312 LYS cc_start: 0.7134 (mmmt) cc_final: 0.6872 (mmtt) REVERT: B 44 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7116 (mt0) REVERT: B 75 GLN cc_start: 0.7698 (mm110) cc_final: 0.6747 (mm-40) REVERT: B 83 ASP cc_start: 0.8084 (t0) cc_final: 0.7838 (t0) REVERT: R 276 ARG cc_start: 0.7459 (mtm-85) cc_final: 0.7196 (ttp80) outliers start: 16 outliers final: 10 residues processed: 154 average time/residue: 1.1431 time to fit residues: 185.3303 Evaluate side-chains 157 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 273 ARG Chi-restraints excluded: chain R residue 316 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.126420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110337 restraints weight = 27930.162| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.36 r_work: 0.3230 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 7067 Z= 0.268 Angle : 0.947 59.200 9632 Z= 0.569 Chirality : 0.043 0.323 1140 Planarity : 0.004 0.053 1190 Dihedral : 5.606 56.112 1205 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.36 % Favored : 97.52 % Rotamer: Outliers : 2.43 % Allowed : 19.89 % Favored : 77.68 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.62 (0.28), residues: 890 helix: 1.59 (0.25), residues: 398 sheet: -0.10 (0.38), residues: 180 loop : -0.74 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.013 0.002 PHE B 199 TYR 0.009 0.001 TYR R 326 ARG 0.006 0.000 ARG R 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3408.23 seconds wall clock time: 60 minutes 13.63 seconds (3613.63 seconds total)