Starting phenix.real_space_refine on Tue Sep 24 04:28:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/09_2024/7t2g_25612.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/09_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_25612/09_2024/7t2g_25612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/09_2024/7t2g_25612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/09_2024/7t2g_25612.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2g_25612/09_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.92, per 1000 atoms: 0.86 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 - 3.00 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: 1.97 Conformation dependent library (CDL) restraints added in 1.3 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: 0.83 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: 2.22 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: 0.00 - 4.04: 9565 4.04 - 8.08: 60 8.08 - 12.12: 6 12.12 - 16.16: 0 16.16 - 20.20: 1 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 3.040 nonbonded pdb=" OD1 ASN B 110 " pdb=" NZ LYS B 127 " model vdw 2.284 3.120 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.300 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.308 3.120 nonbonded pdb=" OD2 ASP R 147 " pdb=" OH TYR R 326 " model vdw 2.314 3.040 ... (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 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=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: 0.870 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.120 Find NCS groups from input model: 0.080 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:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.300 ------------------------------------------------------------------------------- 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 : 0.885 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: 0.9388 time to fit residues: 166.1896 Evaluate side-chains 154 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1593 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= 0.241 Angle : 0.584 5.533 9632 Z= 0.316 Chirality : 0.043 0.155 1140 Planarity : 0.004 0.037 1190 Dihedral : 6.474 58.432 1208 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.43 % Allowed : 11.87 % Favored : 85.69 % 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: 0.88 (0.28), residues: 890 helix: 1.85 (0.26), residues: 390 sheet: 0.21 (0.38), residues: 167 loop : -0.72 (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 62 PHE 0.015 0.002 PHE R 237 TYR 0.009 0.001 TYR R 148 ARG 0.004 0.001 ARG B 251 *********************** 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 187 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 0.818 Fit side-chains REVERT: A 285 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7185 (mt) REVERT: B 75 GLN cc_start: 0.7681 (mm110) cc_final: 0.7119 (mm110) REVERT: B 83 ASP cc_start: 0.8175 (t0) cc_final: 0.7970 (t0) REVERT: R 230 ASN cc_start: 0.7753 (m-40) cc_final: 0.7454 (m-40) REVERT: R 280 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7431 (mtt-85) outliers start: 17 outliers final: 6 residues processed: 174 average time/residue: 1.2533 time to fit residues: 229.4839 Evaluate side-chains 160 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 B residue 33 ILE Chi-restraints excluded: chain R residue 160 THR 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: 0.9990 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 17 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN R 109 ASN R 150 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7067 Z= 0.251 Angle : 0.565 5.628 9632 Z= 0.304 Chirality : 0.042 0.157 1140 Planarity : 0.004 0.037 1190 Dihedral : 6.192 56.307 1208 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.15 % Allowed : 14.88 % Favored : 82.98 % 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: 0.75 (0.27), residues: 890 helix: 1.81 (0.25), residues: 392 sheet: 0.01 (0.37), residues: 167 loop : -0.80 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.014 0.002 PHE B 151 TYR 0.011 0.001 TYR R 149 ARG 0.005 0.001 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 174 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 0.744 Fit side-chains REVERT: A 19 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7234 (pt) REVERT: A 53 MET cc_start: 0.4687 (mtt) cc_final: 0.4118 (tpp) REVERT: A 285 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7140 (mt) REVERT: B 75 GLN cc_start: 0.7678 (mm110) cc_final: 0.6777 (mm-40) REVERT: R 230 ASN cc_start: 0.7732 (m-40) cc_final: 0.7504 (m-40) REVERT: R 280 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7429 (mtt-85) outliers start: 15 outliers final: 4 residues processed: 164 average time/residue: 1.1604 time to fit residues: 200.5660 Evaluate side-chains 158 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 B residue 33 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 280 ARG 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: 3.9990 chunk 41 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** A 311 ASN B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 7067 Z= 0.370 Angle : 0.655 7.150 9632 Z= 0.346 Chirality : 0.045 0.173 1140 Planarity : 0.005 0.034 1190 Dihedral : 6.465 57.721 1208 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.58 % Allowed : 14.88 % 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: 0.42 (0.27), residues: 890 helix: 1.49 (0.25), residues: 392 sheet: -0.16 (0.37), residues: 172 loop : -0.91 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 82 HIS 0.008 0.002 HIS B 54 PHE 0.018 0.002 PHE B 151 TYR 0.016 0.002 TYR R 326 ARG 0.004 0.001 ARG B 150 *********************** 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 177 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 0.816 Fit side-chains REVERT: A 53 MET cc_start: 0.4925 (mtt) cc_final: 0.3854 (mpp) REVERT: A 207 GLU cc_start: 0.7223 (tp30) cc_final: 0.6746 (mm-30) REVERT: A 285 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7141 (mt) REVERT: B 44 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7141 (mt0) REVERT: B 75 GLN cc_start: 0.7723 (mm110) cc_final: 0.6810 (mm-40) REVERT: R 230 ASN cc_start: 0.7772 (m-40) cc_final: 0.7507 (m-40) REVERT: R 246 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7954 (mp) REVERT: R 280 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7452 (mtt-85) outliers start: 25 outliers final: 9 residues processed: 164 average time/residue: 1.1182 time to fit residues: 193.6168 Evaluate side-chains 162 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 31 SER Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 280 ARG Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 316 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 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** R 297 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7067 Z= 0.275 Angle : 0.585 5.700 9632 Z= 0.313 Chirality : 0.043 0.155 1140 Planarity : 0.004 0.036 1190 Dihedral : 6.087 58.027 1206 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.01 % Allowed : 15.59 % Favored : 80.40 % 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: 0.42 (0.27), residues: 890 helix: 1.53 (0.25), residues: 398 sheet: -0.15 (0.37), residues: 167 loop : -1.03 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.015 0.002 PHE B 151 TYR 0.013 0.002 TYR R 326 ARG 0.003 0.000 ARG B 150 *********************** 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 179 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.4812 (mtt) cc_final: 0.3787 (mpp) REVERT: A 207 GLU cc_start: 0.7313 (tp30) cc_final: 0.6869 (mm-30) REVERT: A 285 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7110 (mt) REVERT: B 44 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7148 (mt0) REVERT: B 75 GLN cc_start: 0.7693 (mm110) cc_final: 0.6805 (mm-40) REVERT: B 83 ASP cc_start: 0.8137 (t0) cc_final: 0.7905 (t0) REVERT: R 230 ASN cc_start: 0.7682 (m-40) cc_final: 0.7468 (m-40) REVERT: R 280 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7419 (mtt-85) outliers start: 28 outliers final: 11 residues processed: 165 average time/residue: 1.0885 time to fit residues: 189.7313 Evaluate side-chains 160 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 101 THR 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 273 ARG Chi-restraints excluded: chain R residue 280 ARG Chi-restraints excluded: chain R residue 316 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 0.0030 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2231 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= 0.225 Angle : 0.554 6.438 9632 Z= 0.296 Chirality : 0.042 0.157 1140 Planarity : 0.004 0.036 1190 Dihedral : 5.652 55.181 1206 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.58 % Allowed : 18.31 % 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: 0.52 (0.27), residues: 890 helix: 1.62 (0.25), residues: 402 sheet: -0.19 (0.37), residues: 177 loop : -0.97 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 0.003 0.000 ARG A 208 *********************** 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 172 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.723 Fit side-chains REVERT: A 53 MET cc_start: 0.4696 (mtt) cc_final: 0.3786 (mpp) REVERT: A 207 GLU cc_start: 0.7254 (tp30) cc_final: 0.6830 (mm-30) REVERT: A 285 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7110 (mt) REVERT: A 308 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6869 (mm-30) REVERT: B 44 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7096 (mt0) REVERT: B 75 GLN cc_start: 0.7686 (mm110) cc_final: 0.7350 (mm110) REVERT: B 83 ASP cc_start: 0.8110 (t0) cc_final: 0.7888 (t0) REVERT: B 304 ARG cc_start: 0.7217 (ttm-80) cc_final: 0.6991 (mtp85) REVERT: R 246 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7962 (mp) REVERT: R 343 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6834 (m-80) outliers start: 18 outliers final: 6 residues processed: 161 average time/residue: 1.1361 time to fit residues: 192.7476 Evaluate side-chains 159 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 165 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 7.9990 chunk 48 optimal weight: 0.0040 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 84 optimal weight: 0.0020 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.3600 ------------------------------------------------------------------------------- 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 259 GLN B 293 ASN B 340 ASN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7067 Z= 0.168 Angle : 0.509 6.315 9632 Z= 0.274 Chirality : 0.041 0.158 1140 Planarity : 0.003 0.037 1190 Dihedral : 5.189 54.536 1205 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.72 % Allowed : 20.74 % Favored : 77.54 % 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 (0.28), residues: 890 helix: 1.78 (0.25), residues: 401 sheet: 0.11 (0.38), residues: 167 loop : -0.98 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.013 0.001 PHE R 237 TYR 0.014 0.001 TYR R 149 ARG 0.006 0.000 ARG R 280 *********************** 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 167 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 0.745 Fit side-chains REVERT: A 52 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6942 (mm110) REVERT: A 53 MET cc_start: 0.4406 (mtt) cc_final: 0.3735 (mpp) REVERT: A 207 GLU cc_start: 0.7248 (tp30) cc_final: 0.6841 (mm-30) REVERT: A 308 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6885 (mm-30) REVERT: B 75 GLN cc_start: 0.7667 (mm110) cc_final: 0.7328 (mm110) REVERT: R 276 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7201 (ttp80) REVERT: R 343 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6960 (m-80) outliers start: 12 outliers final: 2 residues processed: 160 average time/residue: 1.1360 time to fit residues: 191.5886 Evaluate side-chains 147 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 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 195 HIS A 244 HIS A 269 ASN B 142 HIS B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7067 Z= 0.215 Angle : 0.544 6.721 9632 Z= 0.291 Chirality : 0.042 0.167 1140 Planarity : 0.004 0.037 1190 Dihedral : 5.405 54.669 1205 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.14 % Allowed : 21.75 % Favored : 77.11 % 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: 0.61 (0.27), residues: 890 helix: 1.73 (0.25), residues: 401 sheet: -0.16 (0.38), residues: 174 loop : -0.95 (0.33), residues: 315 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 151 TYR 0.010 0.001 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 159 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 0.813 Fit side-chains REVERT: A 19 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7153 (pt) REVERT: A 52 GLN cc_start: 0.7129 (mm-40) cc_final: 0.6847 (mm110) REVERT: A 53 MET cc_start: 0.4453 (mtt) cc_final: 0.3712 (mpp) REVERT: A 207 GLU cc_start: 0.7317 (tp30) cc_final: 0.6908 (mm-30) REVERT: A 308 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6863 (mm-30) REVERT: B 75 GLN cc_start: 0.7675 (mm110) cc_final: 0.6778 (mm-40) REVERT: R 276 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7204 (ttp80) REVERT: R 343 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6865 (m-80) outliers start: 8 outliers final: 2 residues processed: 154 average time/residue: 1.2056 time to fit residues: 195.8494 Evaluate side-chains 150 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 B 17 GLN B 142 HIS B 220 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7067 Z= 0.194 Angle : 0.533 6.747 9632 Z= 0.285 Chirality : 0.042 0.177 1140 Planarity : 0.004 0.037 1190 Dihedral : 5.339 54.603 1205 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.43 % Allowed : 21.60 % Favored : 76.97 % 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: 0.59 (0.27), residues: 890 helix: 1.66 (0.25), residues: 401 sheet: -0.12 (0.37), residues: 178 loop : -0.94 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.012 0.001 PHE R 237 TYR 0.016 0.001 TYR R 149 ARG 0.007 0.001 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 160 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.896 Fit side-chains REVERT: A 19 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7171 (pt) REVERT: A 53 MET cc_start: 0.4441 (mtt) cc_final: 0.3733 (mpp) REVERT: A 207 GLU cc_start: 0.7309 (tp30) cc_final: 0.7010 (mm-30) REVERT: A 285 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7065 (mt) REVERT: A 308 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6859 (mm-30) REVERT: B 75 GLN cc_start: 0.7679 (mm110) cc_final: 0.7263 (mm110) REVERT: R 243 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7397 (mpm) REVERT: R 276 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.7204 (ttp80) REVERT: R 343 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6865 (m-80) outliers start: 10 outliers final: 2 residues processed: 151 average time/residue: 1.2288 time to fit residues: 195.4305 Evaluate side-chains 153 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 17 GLN B 142 HIS B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN R 188 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7067 Z= 0.249 Angle : 0.578 6.850 9632 Z= 0.309 Chirality : 0.043 0.187 1140 Planarity : 0.004 0.037 1190 Dihedral : 5.600 55.768 1205 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.14 % Allowed : 22.03 % Favored : 76.82 % 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: 0.48 (0.27), residues: 890 helix: 1.50 (0.25), residues: 401 sheet: -0.11 (0.37), residues: 179 loop : -0.94 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.013 0.002 PHE B 151 TYR 0.011 0.001 TYR R 326 ARG 0.007 0.001 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 156 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 0.883 Fit side-chains REVERT: A 19 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7181 (pt) REVERT: A 52 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6859 (mm110) REVERT: A 53 MET cc_start: 0.4527 (mtt) cc_final: 0.3754 (mpp) REVERT: A 207 GLU cc_start: 0.7269 (tp30) cc_final: 0.6791 (mm-30) REVERT: A 285 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7095 (mt) REVERT: A 308 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6886 (mm-30) REVERT: B 75 GLN cc_start: 0.7683 (mm110) cc_final: 0.6785 (mm-40) REVERT: R 243 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7531 (mpm) REVERT: R 276 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.7198 (ttp80) REVERT: R 343 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6858 (m-80) outliers start: 8 outliers final: 2 residues processed: 150 average time/residue: 1.2015 time to fit residues: 189.9091 Evaluate side-chains 155 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 B 17 GLN B 142 HIS B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111393 restraints weight = 27653.841| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.32 r_work: 0.3253 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2449 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= 0.225 Angle : 0.564 6.752 9632 Z= 0.302 Chirality : 0.042 0.177 1140 Planarity : 0.004 0.037 1190 Dihedral : 5.553 55.341 1205 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.57 % Allowed : 21.17 % Favored : 77.25 % 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: 0.45 (0.27), residues: 890 helix: 1.47 (0.25), residues: 401 sheet: -0.10 (0.37), residues: 179 loop : -0.95 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.012 0.002 PHE B 151 TYR 0.015 0.001 TYR R 149 ARG 0.007 0.001 ARG R 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3439.04 seconds wall clock time: 61 minutes 22.60 seconds (3682.60 seconds total)