Starting phenix.real_space_refine on Fri Nov 15 06:05:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/11_2024/8g59_29736.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/11_2024/8g59_29736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/11_2024/8g59_29736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/11_2024/8g59_29736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/11_2024/8g59_29736.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/11_2024/8g59_29736.cif" } resolution = 2.64 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= 0.008 sd= 0.088 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5503 2.51 5 N 1444 2.21 5 O 1577 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8583 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2509 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "Y" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 365 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "S" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1739 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1739 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 2204 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 2193 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 4 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Conformer: "B" Number of residues, atoms: 281, 2193 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 4 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 bond proxies already assigned to first conformer: 2231 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'YN9': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE R 115 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE R 115 " occ=0.50 Time building chain proxies: 5.82, per 1000 atoms: 0.68 Number of scatterers: 8583 At special positions: 0 Unit cell: (105.456, 121.68, 115.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 F 1 9.00 O 1577 8.00 N 1444 7.00 C 5503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.3 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 37.4% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'Y' and resid 10 through 24 Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 Processing helix chain 'Y' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.619A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.985A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.388A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.367A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.940A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'R' and resid 42 through 70 Processing helix chain 'R' and resid 78 through 91 removed outlier: 3.956A pdb=" N ALA R 91 " --> pdb=" O LEU R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 101 removed outlier: 3.628A pdb=" N VAL R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 142 removed outlier: 4.695A pdb=" N APHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 169 Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.658A pdb=" N PHE R 176 " --> pdb=" O PRO R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 244 removed outlier: 3.556A pdb=" N TRP R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL R 209 " --> pdb=" O ILE R 205 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) Proline residue: R 219 - end of helix removed outlier: 3.958A pdb=" N ARG R 238 " --> pdb=" O THR R 234 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 292 removed outlier: 3.614A pdb=" N LEU R 262 " --> pdb=" O GLN R 258 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE R 263 " --> pdb=" O ASP R 259 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 299 through 321 removed outlier: 3.903A pdb=" N TRP R 305 " --> pdb=" O SER R 301 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.541A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.627A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.826A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.600A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.484A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.593A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.714A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.527A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS S 22 " --> pdb=" O LEU S 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.572A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.559A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.624A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.697A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 177 through 182 437 hydrogen bonds defined for protein. 1231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1365 1.26 - 1.40: 2177 1.40 - 1.53: 4857 1.53 - 1.67: 280 1.67 - 1.81: 84 Bond restraints: 8763 Sorted by residual: bond pdb=" C PHE R 260 " pdb=" O PHE R 260 " ideal model delta sigma weight residual 1.233 1.117 0.116 1.46e-02 4.69e+03 6.29e+01 bond pdb=" N GLN R 258 " pdb=" CA GLN R 258 " ideal model delta sigma weight residual 1.458 1.383 0.074 1.33e-02 5.65e+03 3.12e+01 bond pdb=" N ASP R 259 " pdb=" CA ASP R 259 " ideal model delta sigma weight residual 1.456 1.393 0.063 1.18e-02 7.18e+03 2.84e+01 bond pdb=" C ARG R 36 " pdb=" O ARG R 36 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.25e-02 6.40e+03 2.54e+01 bond pdb=" C1 YN9 R 401 " pdb=" C3 YN9 R 401 " ideal model delta sigma weight residual 1.481 1.581 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 8758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 11696 2.34 - 4.67: 178 4.67 - 7.01: 27 7.01 - 9.35: 5 9.35 - 11.68: 4 Bond angle restraints: 11910 Sorted by residual: angle pdb=" N PHE R 260 " pdb=" CA PHE R 260 " pdb=" C PHE R 260 " ideal model delta sigma weight residual 114.04 102.67 11.37 1.24e+00 6.50e-01 8.41e+01 angle pdb=" C ALA R 91 " pdb=" N ILE R 92 " pdb=" CA ILE R 92 " ideal model delta sigma weight residual 120.24 124.87 -4.63 6.30e-01 2.52e+00 5.39e+01 angle pdb=" N ILE R 89 " pdb=" CA ILE R 89 " pdb=" C ILE R 89 " ideal model delta sigma weight residual 110.62 117.17 -6.55 1.02e+00 9.61e-01 4.13e+01 angle pdb=" N LEU A 358 " pdb=" CA LEU A 358 " pdb=" C LEU A 358 " ideal model delta sigma weight residual 111.36 118.33 -6.97 1.09e+00 8.42e-01 4.09e+01 angle pdb=" C ASP R 259 " pdb=" CA ASP R 259 " pdb=" CB ASP R 259 " ideal model delta sigma weight residual 110.94 120.06 -9.12 1.65e+00 3.67e-01 3.05e+01 ... (remaining 11905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4695 15.94 - 31.87: 368 31.87 - 47.81: 62 47.81 - 63.75: 16 63.75 - 79.68: 7 Dihedral angle restraints: 5148 sinusoidal: 1904 harmonic: 3244 Sorted by residual: dihedral pdb=" C ASP R 259 " pdb=" N ASP R 259 " pdb=" CA ASP R 259 " pdb=" CB ASP R 259 " ideal model delta harmonic sigma weight residual -122.60 -144.58 21.98 0 2.50e+00 1.60e-01 7.73e+01 dihedral pdb=" N ASP R 259 " pdb=" C ASP R 259 " pdb=" CA ASP R 259 " pdb=" CB ASP R 259 " ideal model delta harmonic sigma weight residual 122.80 142.49 -19.69 0 2.50e+00 1.60e-01 6.21e+01 dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 27.64 65.36 1 1.00e+01 1.00e-02 5.60e+01 ... (remaining 5145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 1389 0.197 - 0.394: 3 0.394 - 0.591: 0 0.591 - 0.788: 0 0.788 - 0.985: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ASP R 259 " pdb=" N ASP R 259 " pdb=" C ASP R 259 " pdb=" CB ASP R 259 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CA ARG R 254 " pdb=" N ARG R 254 " pdb=" C ARG R 254 " pdb=" CB ARG R 254 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA GLN R 258 " pdb=" N GLN R 258 " pdb=" C GLN R 258 " pdb=" CB GLN R 258 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1390 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 257 " -0.028 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C GLN R 257 " 0.098 2.00e-02 2.50e+03 pdb=" O GLN R 257 " -0.037 2.00e-02 2.50e+03 pdb=" N GLN R 258 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO S 75 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 299 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO R 300 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO R 300 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 300 " 0.034 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 57 2.52 - 3.12: 6315 3.12 - 3.71: 13279 3.71 - 4.31: 19213 4.31 - 4.90: 32205 Nonbonded interactions: 71069 Sorted by model distance: nonbonded pdb=" NH2 ARG R 238 " pdb=" OD2 ASP R 259 " model vdw 1.930 3.120 nonbonded pdb=" O CYS R 60 " pdb=" CD2 LEU R 64 " model vdw 1.953 3.460 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.183 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.222 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.255 3.120 ... (remaining 71064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.370 Find NCS groups from input model: 0.080 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 8763 Z= 0.334 Angle : 0.728 11.682 11910 Z= 0.430 Chirality : 0.053 0.985 1393 Planarity : 0.006 0.112 1491 Dihedral : 12.174 79.684 3040 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 0.22 % Allowed : 0.88 % Favored : 98.90 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % 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: -0.15 (0.25), residues: 1095 helix: 0.23 (0.25), residues: 387 sheet: 0.39 (0.30), residues: 301 loop : -0.65 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 63 HIS 0.004 0.001 HIS R 251 PHE 0.016 0.001 PHE R 311 TYR 0.017 0.001 TYR A 302 ARG 0.007 0.000 ARG R 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 209 LYS cc_start: 0.9253 (mttm) cc_final: 0.9006 (mttp) REVERT: R 165 TYR cc_start: 0.7006 (t80) cc_final: 0.6178 (t80) outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 1.5725 time to fit residues: 266.4302 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 259 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 0.0470 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 230 ASN B 268 ASN B 340 ASN S 179 GLN S 186 GLN A 204 GLN A 357 ASN R 189 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8763 Z= 0.194 Angle : 0.622 10.651 11910 Z= 0.318 Chirality : 0.043 0.140 1393 Planarity : 0.005 0.074 1491 Dihedral : 5.137 59.470 1212 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.21 % Allowed : 10.46 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.53 (0.26), residues: 1095 helix: 1.13 (0.27), residues: 376 sheet: 0.53 (0.31), residues: 297 loop : -0.38 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.004 0.001 HIS A 195 PHE 0.017 0.001 PHE R 263 TYR 0.015 0.001 TYR S 190 ARG 0.007 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8024 (ppp) REVERT: B 186 ASP cc_start: 0.7681 (m-30) cc_final: 0.7355 (m-30) REVERT: B 335 PHE cc_start: 0.8661 (m-80) cc_final: 0.8431 (m-80) REVERT: A 193 ASP cc_start: 0.7945 (p0) cc_final: 0.7733 (p0) REVERT: R 165 TYR cc_start: 0.7002 (t80) cc_final: 0.5933 (t80) REVERT: R 240 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.5632 (ptt90) outliers start: 11 outliers final: 2 residues processed: 151 average time/residue: 1.5070 time to fit residues: 239.7401 Evaluate side-chains 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain R residue 240 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 83 optimal weight: 0.0870 chunk 68 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN B 268 ASN S 194 ASN A 188 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8763 Z= 0.168 Angle : 0.568 10.106 11910 Z= 0.291 Chirality : 0.042 0.132 1393 Planarity : 0.005 0.062 1491 Dihedral : 4.406 38.812 1210 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.32 % Allowed : 13.33 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1095 helix: 1.41 (0.27), residues: 377 sheet: 0.72 (0.32), residues: 284 loop : -0.35 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS A 195 PHE 0.009 0.001 PHE R 51 TYR 0.013 0.001 TYR S 190 ARG 0.011 0.001 ARG R 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8113 (mptm) REVERT: B 228 ASP cc_start: 0.7904 (p0) cc_final: 0.7615 (p0) REVERT: A 240 MET cc_start: 0.6639 (ptt) cc_final: 0.6266 (ptp) REVERT: R 165 TYR cc_start: 0.7009 (t80) cc_final: 0.5884 (t80) outliers start: 12 outliers final: 2 residues processed: 135 average time/residue: 1.5343 time to fit residues: 218.1020 Evaluate side-chains 132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8763 Z= 0.215 Angle : 0.585 10.960 11910 Z= 0.297 Chirality : 0.042 0.144 1393 Planarity : 0.005 0.060 1491 Dihedral : 4.600 43.575 1210 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.98 % Allowed : 14.76 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.70 (0.26), residues: 1095 helix: 1.25 (0.27), residues: 384 sheet: 0.69 (0.31), residues: 292 loop : -0.35 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 63 HIS 0.005 0.001 HIS A 188 PHE 0.022 0.001 PHE R 260 TYR 0.012 0.001 TYR S 190 ARG 0.009 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7426 (mtp85) REVERT: A 193 ASP cc_start: 0.7922 (p0) cc_final: 0.7683 (p0) REVERT: A 240 MET cc_start: 0.6573 (ptt) cc_final: 0.6276 (ptp) REVERT: R 165 TYR cc_start: 0.7046 (t80) cc_final: 0.5923 (t80) outliers start: 18 outliers final: 5 residues processed: 143 average time/residue: 1.4653 time to fit residues: 221.1809 Evaluate side-chains 130 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 0.0070 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8763 Z= 0.167 Angle : 0.558 8.721 11910 Z= 0.285 Chirality : 0.041 0.127 1393 Planarity : 0.005 0.059 1491 Dihedral : 4.327 39.350 1210 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.43 % Allowed : 16.41 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.86 (0.26), residues: 1095 helix: 1.48 (0.27), residues: 389 sheet: 0.69 (0.31), residues: 292 loop : -0.30 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.016 0.001 PHE R 260 TYR 0.011 0.001 TYR S 190 ARG 0.010 0.001 ARG R 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7408 (mtp85) REVERT: B 78 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8108 (mptm) REVERT: A 240 MET cc_start: 0.6570 (ptt) cc_final: 0.6267 (ptp) REVERT: R 165 TYR cc_start: 0.7036 (t80) cc_final: 0.5933 (t80) outliers start: 13 outliers final: 5 residues processed: 140 average time/residue: 1.5452 time to fit residues: 227.6660 Evaluate side-chains 146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8763 Z= 0.183 Angle : 0.565 10.882 11910 Z= 0.287 Chirality : 0.041 0.137 1393 Planarity : 0.005 0.059 1491 Dihedral : 4.388 39.471 1210 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.87 % Allowed : 17.07 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.96 (0.26), residues: 1095 helix: 1.60 (0.27), residues: 387 sheet: 0.70 (0.30), residues: 292 loop : -0.25 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.020 0.001 PHE R 263 TYR 0.011 0.001 TYR S 190 ARG 0.009 0.001 ARG R 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7400 (mtp85) REVERT: B 259 GLN cc_start: 0.8301 (tt0) cc_final: 0.8094 (mt0) REVERT: A 193 ASP cc_start: 0.7907 (p0) cc_final: 0.7650 (p0) REVERT: A 240 MET cc_start: 0.6588 (ptt) cc_final: 0.6308 (ptp) REVERT: R 165 TYR cc_start: 0.7078 (t80) cc_final: 0.5937 (t80) REVERT: R 323 MET cc_start: 0.4961 (mmm) cc_final: 0.4522 (mtm) outliers start: 17 outliers final: 6 residues processed: 143 average time/residue: 1.4940 time to fit residues: 225.4771 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain R residue 180 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 0.0270 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8763 Z= 0.302 Angle : 0.632 11.472 11910 Z= 0.321 Chirality : 0.044 0.149 1393 Planarity : 0.005 0.064 1491 Dihedral : 4.659 40.894 1210 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.09 % Allowed : 16.85 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.73 (0.26), residues: 1095 helix: 1.26 (0.27), residues: 387 sheet: 0.71 (0.31), residues: 292 loop : -0.32 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 104 HIS 0.005 0.001 HIS B 142 PHE 0.015 0.002 PHE R 177 TYR 0.011 0.001 TYR R 165 ARG 0.010 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7426 (mtp85) REVERT: B 78 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8116 (mptm) REVERT: A 240 MET cc_start: 0.6770 (ptt) cc_final: 0.6506 (ptp) REVERT: R 165 TYR cc_start: 0.7215 (t80) cc_final: 0.7007 (t80) REVERT: R 240 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6307 (ptp90) REVERT: R 290 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7328 (pt0) outliers start: 19 outliers final: 8 residues processed: 141 average time/residue: 1.6011 time to fit residues: 236.9225 Evaluate side-chains 146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 240 ARG Chi-restraints excluded: chain R residue 290 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8763 Z= 0.171 Angle : 0.571 8.746 11910 Z= 0.292 Chirality : 0.041 0.137 1393 Planarity : 0.005 0.061 1491 Dihedral : 4.368 32.911 1210 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.65 % Allowed : 17.62 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.97 (0.26), residues: 1095 helix: 1.70 (0.27), residues: 382 sheet: 0.66 (0.30), residues: 294 loop : -0.29 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.022 0.001 PHE R 263 TYR 0.011 0.001 TYR S 190 ARG 0.009 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7433 (mtp85) REVERT: R 165 TYR cc_start: 0.7068 (t80) cc_final: 0.5917 (t80) REVERT: R 240 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6346 (ptp90) outliers start: 15 outliers final: 7 residues processed: 150 average time/residue: 1.5166 time to fit residues: 239.7917 Evaluate side-chains 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain R residue 240 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8763 Z= 0.301 Angle : 0.653 11.774 11910 Z= 0.331 Chirality : 0.044 0.154 1393 Planarity : 0.005 0.064 1491 Dihedral : 4.622 36.410 1210 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.98 % Allowed : 17.73 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.26), residues: 1095 helix: 1.33 (0.27), residues: 387 sheet: 0.72 (0.30), residues: 294 loop : -0.25 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 104 HIS 0.006 0.001 HIS R 251 PHE 0.015 0.002 PHE R 177 TYR 0.011 0.002 TYR R 165 ARG 0.010 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7416 (mtp85) REVERT: B 127 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8809 (mptt) REVERT: R 165 TYR cc_start: 0.7204 (t80) cc_final: 0.6991 (t80) REVERT: R 240 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6181 (ptp90) outliers start: 18 outliers final: 8 residues processed: 137 average time/residue: 1.5935 time to fit residues: 229.8971 Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 240 ARG Chi-restraints excluded: chain R residue 323 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8763 Z= 0.194 Angle : 0.603 9.440 11910 Z= 0.308 Chirality : 0.042 0.147 1393 Planarity : 0.005 0.061 1491 Dihedral : 4.433 31.566 1210 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.21 % Allowed : 18.61 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.94 (0.26), residues: 1095 helix: 1.57 (0.27), residues: 387 sheet: 0.73 (0.31), residues: 292 loop : -0.27 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 63 HIS 0.004 0.001 HIS A 188 PHE 0.021 0.001 PHE R 263 TYR 0.011 0.001 TYR S 190 ARG 0.010 0.001 ARG R 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7429 (mtp85) REVERT: S 192 MET cc_start: 0.8708 (ttp) cc_final: 0.8415 (tmm) REVERT: A 240 MET cc_start: 0.5557 (ptp) cc_final: 0.4939 (ttm) REVERT: R 165 TYR cc_start: 0.7088 (t80) cc_final: 0.5926 (t80) REVERT: R 240 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6238 (ptp90) outliers start: 11 outliers final: 9 residues processed: 146 average time/residue: 1.4997 time to fit residues: 231.4882 Evaluate side-chains 143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain R residue 240 ARG Chi-restraints excluded: chain R residue 323 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.149118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.113280 restraints weight = 20346.202| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.36 r_work: 0.3558 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8763 Z= 0.246 Angle : 0.630 11.488 11910 Z= 0.320 Chirality : 0.043 0.149 1393 Planarity : 0.005 0.062 1491 Dihedral : 4.467 31.856 1210 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.43 % Allowed : 18.72 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.91 (0.26), residues: 1095 helix: 1.52 (0.27), residues: 387 sheet: 0.71 (0.31), residues: 292 loop : -0.25 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 63 HIS 0.004 0.001 HIS A 188 PHE 0.012 0.001 PHE R 260 TYR 0.013 0.001 TYR B 264 ARG 0.010 0.001 ARG R 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4277.45 seconds wall clock time: 76 minutes 51.59 seconds (4611.59 seconds total)