Starting phenix.real_space_refine on Wed Feb 14 09:48:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2g_34437/02_2024/8h2g_34437_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2g_34437/02_2024/8h2g_34437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2g_34437/02_2024/8h2g_34437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2g_34437/02_2024/8h2g_34437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2g_34437/02_2024/8h2g_34437_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2g_34437/02_2024/8h2g_34437_updated.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.059 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 64 5.16 5 C 5756 2.51 5 N 1540 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9023 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2365 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.31, per 1000 atoms: 0.59 Number of scatterers: 9023 At special positions: 0 Unit cell: (88.395, 122.01, 131.97, 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 64 16.00 O 1663 8.00 N 1540 7.00 C 5756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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: 3.46 Conformation dependent library (CDL) restraints added in 1.7 seconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 14 sheets defined 31.4% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 removed outlier: 4.098A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 88 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 98 through 130 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.639A pdb=" N LYS A 164 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 217 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 226 through 260 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 270 through 294 removed outlier: 4.060A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.879A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.798A pdb=" N SER B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.768A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 351 removed outlier: 3.855A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.511A pdb=" N THR C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= B, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.354A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLY B 40 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 49 through 52 removed outlier: 4.335A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.785A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.744A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.690A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.629A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.460A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.661A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 5 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 93 through 99 removed outlier: 5.708A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.548A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.560A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.629A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2913 1.35 - 1.47: 2298 1.47 - 1.59: 3917 1.59 - 1.71: 0 1.71 - 1.83: 92 Bond restraints: 9220 Sorted by residual: bond pdb=" C2 NIO A 401 " pdb=" C3 NIO A 401 " ideal model delta sigma weight residual 1.390 1.351 0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" C3 NIO A 401 " pdb=" C4 NIO A 401 " ideal model delta sigma weight residual 1.386 1.353 0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C ILE A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.36e-02 5.41e+03 2.49e+00 bond pdb=" CB GLU E 89 " pdb=" CG GLU E 89 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CG ARG B 32 " pdb=" CD ARG B 32 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 9215 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.28: 179 106.28 - 113.22: 4985 113.22 - 120.16: 3192 120.16 - 127.11: 4018 127.11 - 134.05: 102 Bond angle restraints: 12476 Sorted by residual: angle pdb=" C ASP A 97 " pdb=" N ILE A 98 " pdb=" CA ILE A 98 " ideal model delta sigma weight residual 120.24 122.61 -2.37 6.30e-01 2.52e+00 1.41e+01 angle pdb=" C ILE A 98 " pdb=" CA ILE A 98 " pdb=" CB ILE A 98 " ideal model delta sigma weight residual 114.35 110.94 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" CA TRP A 256 " pdb=" CB TRP A 256 " pdb=" CG TRP A 256 " ideal model delta sigma weight residual 113.60 119.62 -6.02 1.90e+00 2.77e-01 1.01e+01 angle pdb=" CB GLU E 89 " pdb=" CG GLU E 89 " pdb=" CD GLU E 89 " ideal model delta sigma weight residual 112.60 117.35 -4.75 1.70e+00 3.46e-01 7.79e+00 angle pdb=" CA LEU A 195 " pdb=" CB LEU A 195 " pdb=" CG LEU A 195 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.73e+00 ... (remaining 12471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4656 17.92 - 35.83: 625 35.83 - 53.75: 154 53.75 - 71.67: 20 71.67 - 89.58: 8 Dihedral angle restraints: 5463 sinusoidal: 2146 harmonic: 3317 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual -86.00 -156.72 70.72 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CA LEU B 268 " pdb=" C LEU B 268 " pdb=" N ASN B 269 " pdb=" CA ASN B 269 " ideal model delta harmonic sigma weight residual 180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -118.16 32.16 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 887 0.031 - 0.062: 331 0.062 - 0.093: 107 0.093 - 0.124: 63 0.124 - 0.155: 12 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB ILE A 78 " pdb=" CA ILE A 78 " pdb=" CG1 ILE A 78 " pdb=" CG2 ILE A 78 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CG LEU A 195 " pdb=" CB LEU A 195 " pdb=" CD1 LEU A 195 " pdb=" CD2 LEU A 195 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ASN A 171 " pdb=" N ASN A 171 " pdb=" C ASN A 171 " pdb=" CB ASN A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1397 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 171 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ASN A 171 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 171 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 172 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 199 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 200 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 192 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C MET E 192 " -0.029 2.00e-02 2.50e+03 pdb=" O MET E 192 " 0.011 2.00e-02 2.50e+03 pdb=" N SER E 193 " 0.010 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 9 2.27 - 2.93: 3917 2.93 - 3.59: 12827 3.59 - 4.24: 20593 4.24 - 4.90: 36282 Nonbonded interactions: 73628 Sorted by model distance: nonbonded pdb=" NH1 ARG A 218 " pdb=" CD1 ILE B 344 " model vdw 1.613 3.540 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.123 2.440 nonbonded pdb=" CB SER A 298 " pdb=" O GLY B 352 " model vdw 2.153 3.440 nonbonded pdb=" O ASN A 171 " pdb=" ND2 ASN A 171 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.226 2.440 ... (remaining 73623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.490 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: 2.270 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.930 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.003 0.041 9220 Z= 0.203 Angle : 0.567 9.733 12476 Z= 0.299 Chirality : 0.042 0.155 1400 Planarity : 0.004 0.047 1580 Dihedral : 16.846 89.584 3304 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.61 % Allowed : 29.29 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.07 (0.26), residues: 1131 helix: 1.59 (0.28), residues: 377 sheet: -0.23 (0.34), residues: 264 loop : -0.99 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 93 HIS 0.004 0.001 HIS A 184 PHE 0.021 0.001 PHE A 95 TYR 0.021 0.001 TYR B 302 ARG 0.015 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.6779 (m) cc_final: 0.6543 (m) REVERT: A 154 ILE cc_start: 0.7938 (mt) cc_final: 0.7725 (mt) outliers start: 6 outliers final: 3 residues processed: 155 average time/residue: 0.2084 time to fit residues: 45.0037 Evaluate side-chains 125 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 38 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 HIS A 171 ASN A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9220 Z= 0.391 Angle : 0.692 8.319 12476 Z= 0.356 Chirality : 0.047 0.182 1400 Planarity : 0.005 0.047 1580 Dihedral : 4.857 31.113 1241 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 7.86 % Allowed : 25.10 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.12 (0.25), residues: 1131 helix: 1.51 (0.27), residues: 374 sheet: -0.26 (0.32), residues: 264 loop : -1.21 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 93 HIS 0.007 0.002 HIS E 35 PHE 0.022 0.002 PHE A 105 TYR 0.018 0.002 TYR E 190 ARG 0.011 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 133 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.6982 (m) cc_final: 0.6705 (m) REVERT: A 104 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6034 (mt) REVERT: A 112 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: A 120 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8269 (t) REVERT: A 234 MET cc_start: 0.6980 (mmm) cc_final: 0.6667 (tpt) REVERT: B 33 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6817 (tt0) REVERT: C 44 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: C 251 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8251 (mtt-85) REVERT: E 89 GLU cc_start: 0.7545 (pp20) cc_final: 0.7218 (pp20) outliers start: 77 outliers final: 43 residues processed: 192 average time/residue: 0.1929 time to fit residues: 52.6301 Evaluate side-chains 173 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 124 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 223 HIS B 244 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9220 Z= 0.191 Angle : 0.541 6.788 12476 Z= 0.284 Chirality : 0.042 0.156 1400 Planarity : 0.004 0.041 1580 Dihedral : 4.373 29.269 1236 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.90 % Allowed : 26.94 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.02 (0.25), residues: 1131 helix: 1.73 (0.28), residues: 372 sheet: -0.28 (0.31), residues: 269 loop : -1.16 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.004 0.001 HIS C 91 PHE 0.011 0.001 PHE B 334 TYR 0.016 0.001 TYR B 302 ARG 0.006 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7214 (tt0) REVERT: A 120 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8253 (t) REVERT: A 234 MET cc_start: 0.6943 (mmm) cc_final: 0.6644 (tpt) REVERT: B 249 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7594 (tt) REVERT: C 44 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6734 (mp10) REVERT: C 234 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: E 89 GLU cc_start: 0.7473 (pp20) cc_final: 0.7136 (pp20) outliers start: 48 outliers final: 27 residues processed: 174 average time/residue: 0.2081 time to fit residues: 50.6121 Evaluate side-chains 161 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0980 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 102 optimal weight: 0.0980 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 161 HIS A 223 HIS B 244 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9220 Z= 0.159 Angle : 0.515 6.820 12476 Z= 0.271 Chirality : 0.041 0.161 1400 Planarity : 0.003 0.040 1580 Dihedral : 4.184 26.251 1236 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 6.02 % Allowed : 26.22 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.09 (0.25), residues: 1131 helix: 1.74 (0.27), residues: 374 sheet: -0.18 (0.31), residues: 268 loop : -1.12 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE A 38 TYR 0.015 0.001 TYR B 302 ARG 0.008 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 133 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7288 (tt0) REVERT: A 120 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8238 (t) REVERT: A 165 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6022 (tptt) REVERT: A 201 LEU cc_start: 0.5101 (OUTLIER) cc_final: 0.4515 (tp) REVERT: A 234 MET cc_start: 0.6969 (mmm) cc_final: 0.6667 (tpt) REVERT: B 249 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7523 (tt) REVERT: C 234 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: E 89 GLU cc_start: 0.7406 (pp20) cc_final: 0.7069 (pp20) REVERT: E 189 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7934 (mt) outliers start: 59 outliers final: 37 residues processed: 175 average time/residue: 0.1938 time to fit residues: 48.0253 Evaluate side-chains 170 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.0570 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 45 ASN A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 : 0.006 0.059 9220 Z= 0.418 Angle : 0.656 7.687 12476 Z= 0.342 Chirality : 0.047 0.155 1400 Planarity : 0.004 0.051 1580 Dihedral : 4.708 27.585 1236 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 7.86 % Allowed : 25.20 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.13 (0.25), residues: 1131 helix: 1.53 (0.27), residues: 374 sheet: -0.28 (0.31), residues: 268 loop : -1.25 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 93 HIS 0.006 0.001 HIS C 142 PHE 0.017 0.002 PHE A 117 TYR 0.018 0.002 TYR B 302 ARG 0.010 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 135 time to evaluate : 1.119 Fit side-chains REVERT: A 38 PHE cc_start: 0.6611 (t80) cc_final: 0.6410 (t80) REVERT: A 112 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: A 120 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8348 (t) REVERT: A 165 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6133 (tptm) REVERT: B 33 GLU cc_start: 0.7110 (tt0) cc_final: 0.6902 (tt0) REVERT: C 44 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: C 234 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: C 251 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8214 (mtt-85) REVERT: C 336 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8097 (mp) REVERT: E 234 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7425 (mm-30) outliers start: 77 outliers final: 59 residues processed: 193 average time/residue: 0.2247 time to fit residues: 59.6459 Evaluate side-chains 198 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 131 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9220 Z= 0.205 Angle : 0.557 8.655 12476 Z= 0.290 Chirality : 0.042 0.148 1400 Planarity : 0.004 0.040 1580 Dihedral : 4.429 27.194 1236 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 7.24 % Allowed : 25.20 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.01 (0.25), residues: 1131 helix: 1.66 (0.27), residues: 374 sheet: -0.21 (0.31), residues: 263 loop : -1.20 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS C 91 PHE 0.011 0.001 PHE A 232 TYR 0.017 0.001 TYR B 302 ARG 0.008 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 131 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7529 (tt0) REVERT: A 120 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8308 (t) REVERT: A 165 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6116 (tptt) REVERT: B 33 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6903 (tt0) REVERT: C 234 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: E 234 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7442 (mm-30) outliers start: 71 outliers final: 54 residues processed: 184 average time/residue: 0.2114 time to fit residues: 54.5723 Evaluate side-chains 187 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 128 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.0070 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 0.0060 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 0.9618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 244 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9220 Z= 0.206 Angle : 0.557 8.094 12476 Z= 0.287 Chirality : 0.042 0.148 1400 Planarity : 0.003 0.040 1580 Dihedral : 4.354 25.451 1236 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 7.24 % Allowed : 25.31 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.01 (0.25), residues: 1131 helix: 1.67 (0.27), residues: 374 sheet: -0.23 (0.31), residues: 268 loop : -1.16 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 93 HIS 0.004 0.001 HIS C 91 PHE 0.015 0.001 PHE A 38 TYR 0.020 0.001 TYR B 302 ARG 0.005 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 130 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7451 (tt0) REVERT: A 120 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8303 (t) REVERT: A 165 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6132 (tptt) REVERT: B 33 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: C 44 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6570 (mp10) REVERT: C 234 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8485 (m-80) REVERT: C 290 ASP cc_start: 0.5746 (OUTLIER) cc_final: 0.5314 (p0) REVERT: E 87 ARG cc_start: 0.8001 (mpt-90) cc_final: 0.7742 (mpt-90) REVERT: E 234 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7427 (mm-30) outliers start: 71 outliers final: 58 residues processed: 183 average time/residue: 0.1974 time to fit residues: 51.1643 Evaluate side-chains 190 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 125 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9220 Z= 0.320 Angle : 0.622 8.672 12476 Z= 0.320 Chirality : 0.045 0.237 1400 Planarity : 0.004 0.054 1580 Dihedral : 4.595 24.533 1236 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 7.96 % Allowed : 25.10 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.13 (0.25), residues: 1131 helix: 1.53 (0.27), residues: 374 sheet: -0.33 (0.31), residues: 270 loop : -1.21 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 93 HIS 0.005 0.001 HIS C 91 PHE 0.015 0.002 PHE E 212 TYR 0.022 0.002 TYR B 302 ARG 0.013 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 132 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.6266 (mtt90) cc_final: 0.6030 (mtm110) REVERT: A 112 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: A 120 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8333 (t) REVERT: A 165 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6147 (tptt) REVERT: B 32 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7448 (ptp-110) REVERT: B 33 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6837 (tt0) REVERT: C 44 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6661 (mp10) REVERT: C 234 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: C 290 ASP cc_start: 0.5947 (OUTLIER) cc_final: 0.5568 (p0) REVERT: E 87 ARG cc_start: 0.8020 (mpt-90) cc_final: 0.7760 (mpt-90) REVERT: E 234 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7466 (mm-30) outliers start: 78 outliers final: 66 residues processed: 190 average time/residue: 0.1986 time to fit residues: 52.6280 Evaluate side-chains 200 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 126 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 244 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9220 Z= 0.282 Angle : 0.609 9.307 12476 Z= 0.312 Chirality : 0.044 0.225 1400 Planarity : 0.004 0.050 1580 Dihedral : 4.558 23.536 1236 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 8.06 % Allowed : 25.20 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.14 (0.25), residues: 1131 helix: 1.56 (0.27), residues: 370 sheet: -0.36 (0.31), residues: 270 loop : -1.21 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 93 HIS 0.005 0.001 HIS C 91 PHE 0.013 0.002 PHE E 212 TYR 0.024 0.002 TYR B 302 ARG 0.011 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 130 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.6256 (mtt90) cc_final: 0.6025 (mtm110) REVERT: A 112 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: A 120 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8332 (t) REVERT: A 165 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6107 (tptt) REVERT: B 33 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: C 44 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6572 (mp10) REVERT: C 234 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: E 234 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7446 (mm-30) outliers start: 79 outliers final: 68 residues processed: 186 average time/residue: 0.2010 time to fit residues: 52.6337 Evaluate side-chains 203 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 128 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 73 optimal weight: 0.1980 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 244 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9220 Z= 0.157 Angle : 0.545 9.683 12476 Z= 0.279 Chirality : 0.041 0.247 1400 Planarity : 0.004 0.060 1580 Dihedral : 4.212 21.996 1236 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.53 % Allowed : 26.73 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.09 (0.25), residues: 1131 helix: 1.72 (0.28), residues: 371 sheet: -0.20 (0.31), residues: 268 loop : -1.08 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 188 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 38 TYR 0.022 0.001 TYR B 302 ARG 0.012 0.000 ARG B 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 139 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: A 120 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8300 (t) REVERT: A 165 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6110 (tptt) REVERT: A 218 ARG cc_start: 0.7222 (ttm-80) cc_final: 0.6958 (ptm160) REVERT: B 32 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7472 (ptp-110) REVERT: B 209 LYS cc_start: 0.8242 (pttm) cc_final: 0.6931 (mmtm) REVERT: B 302 TYR cc_start: 0.6339 (t80) cc_final: 0.6085 (t80) REVERT: B 324 THR cc_start: 0.6681 (m) cc_final: 0.6183 (p) REVERT: B 334 PHE cc_start: 0.7805 (t80) cc_final: 0.7552 (t80) REVERT: C 234 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8506 (m-80) outliers start: 64 outliers final: 55 residues processed: 182 average time/residue: 0.2036 time to fit residues: 52.0190 Evaluate side-chains 192 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 133 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 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 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.207922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170157 restraints weight = 10016.487| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.52 r_work: 0.3603 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9220 Z= 0.197 Angle : 0.563 9.598 12476 Z= 0.288 Chirality : 0.042 0.237 1400 Planarity : 0.004 0.058 1580 Dihedral : 4.237 20.375 1236 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.02 % Allowed : 27.04 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.09 (0.25), residues: 1131 helix: 1.70 (0.27), residues: 371 sheet: -0.18 (0.31), residues: 268 loop : -1.06 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 188 HIS 0.004 0.001 HIS C 91 PHE 0.012 0.001 PHE A 38 TYR 0.023 0.001 TYR B 302 ARG 0.011 0.000 ARG B 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.63 seconds wall clock time: 39 minutes 21.72 seconds (2361.72 seconds total)