Starting phenix.real_space_refine on Wed Aug 5 02:49:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc4_37430/08_2026/8wc4_37430_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc4_37430/08_2026/8wc4_37430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wc4_37430/08_2026/8wc4_37430_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc4_37430/08_2026/8wc4_37430_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wc4_37430/08_2026/8wc4_37430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc4_37430/08_2026/8wc4_37430.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.079 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 Br 1 7.06 5 S 56 5.16 5 C 5369 2.51 5 N 1426 2.21 5 O 1542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1844 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2484 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 7, 'GLU:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2054 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "S" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1622 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "Y" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 380 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.93, per 1000 atoms: 0.23 Number of scatterers: 8394 At special positions: 0 Unit cell: (89.25, 118.15, 124.95, 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) Br 1 34.99 S 56 16.00 O 1542 8.00 N 1426 7.00 C 5369 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.72 Conformation dependent library (CDL) restraints added in 424.9 milliseconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.680A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.539A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.844A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.676A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.729A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.596A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 317 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.639A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 49 removed outlier: 3.721A pdb=" N ILE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE R 44 " --> pdb=" O ASN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 85 removed outlier: 4.223A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 94 through 126 removed outlier: 3.731A pdb=" N ALA R 123 " --> pdb=" O ASP R 119 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 135 through 160 removed outlier: 3.573A pdb=" N ILE R 139 " --> pdb=" O ASN R 135 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL R 141 " --> pdb=" O SER R 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET R 142 " --> pdb=" O THR R 138 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 175 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 198 through 226 removed outlier: 3.538A pdb=" N ILE R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 275 removed outlier: 3.587A pdb=" N THR R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 302 removed outlier: 4.043A pdb=" N ASN R 283 " --> pdb=" O PRO R 279 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR R 291 " --> pdb=" O TYR R 287 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 313 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.666A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.903A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.654A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 45 removed outlier: 3.604A pdb=" N ASP Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 190 removed outlier: 3.541A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.728A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.042A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.902A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.574A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.564A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.571A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.608A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 4 removed outlier: 3.693A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.658A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.566A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.445A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.577A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1077 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: 1.35 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 1357 1.31 - 1.47: 3583 1.47 - 1.63: 3558 1.63 - 1.78: 7 1.78 - 1.94: 75 Bond restraints: 8580 Sorted by residual: bond pdb=" C PRO R 56 " pdb=" O PRO R 56 " ideal model delta sigma weight residual 1.238 1.158 0.080 1.24e-02 6.50e+03 4.16e+01 bond pdb=" C MET R 195 " pdb=" O MET R 195 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.16e-02 7.43e+03 2.59e+01 bond pdb=" CA ASN A 231 " pdb=" C ASN A 231 " ideal model delta sigma weight residual 1.525 1.474 0.051 1.02e-02 9.61e+03 2.49e+01 bond pdb=" C ASP B 312 " pdb=" O ASP B 312 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.38e-02 5.25e+03 2.46e+01 bond pdb=" CA PHE R 50 " pdb=" C PHE R 50 " ideal model delta sigma weight residual 1.524 1.490 0.034 7.00e-03 2.04e+04 2.41e+01 ... (remaining 8575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 11535 3.09 - 6.18: 112 6.18 - 9.27: 16 9.27 - 12.36: 2 12.36 - 15.44: 1 Bond angle restraints: 11666 Sorted by residual: angle pdb=" N GLN R 52 " pdb=" CA GLN R 52 " pdb=" C GLN R 52 " ideal model delta sigma weight residual 112.45 97.01 15.44 1.39e+00 5.18e-01 1.23e+02 angle pdb=" C ILE R 223 " pdb=" CA ILE R 223 " pdb=" CB ILE R 223 " ideal model delta sigma weight residual 111.70 102.14 9.56 1.28e+00 6.10e-01 5.58e+01 angle pdb=" N ALA R 311 " pdb=" CA ALA R 311 " pdb=" C ALA R 311 " ideal model delta sigma weight residual 112.90 103.86 9.04 1.31e+00 5.83e-01 4.76e+01 angle pdb=" C THR R 55 " pdb=" N PRO R 56 " pdb=" CA PRO R 56 " ideal model delta sigma weight residual 119.28 126.65 -7.37 1.10e+00 8.26e-01 4.49e+01 angle pdb=" N TYR R 305 " pdb=" CA TYR R 305 " pdb=" C TYR R 305 " ideal model delta sigma weight residual 109.72 117.84 -8.12 1.25e+00 6.40e-01 4.22e+01 ... (remaining 11661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4569 16.03 - 32.05: 349 32.05 - 48.08: 75 48.08 - 64.11: 12 64.11 - 80.13: 14 Dihedral angle restraints: 5019 sinusoidal: 1794 harmonic: 3225 Sorted by residual: dihedral pdb=" N LYS R 51 " pdb=" C LYS R 51 " pdb=" CA LYS R 51 " pdb=" CB LYS R 51 " ideal model delta harmonic sigma weight residual 122.80 139.77 -16.97 0 2.50e+00 1.60e-01 4.61e+01 dihedral pdb=" C LYS R 51 " pdb=" N LYS R 51 " pdb=" CA LYS R 51 " pdb=" CB LYS R 51 " ideal model delta harmonic sigma weight residual -122.60 -136.57 13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C ILE R 45 " pdb=" N ILE R 45 " pdb=" CA ILE R 45 " pdb=" CB ILE R 45 " ideal model delta harmonic sigma weight residual -122.00 -134.17 12.17 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 5016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1293 0.120 - 0.239: 39 0.239 - 0.359: 5 0.359 - 0.478: 3 0.478 - 0.598: 1 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA LYS R 51 " pdb=" N LYS R 51 " pdb=" C LYS R 51 " pdb=" CB LYS R 51 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" CA PHE R 50 " pdb=" N PHE R 50 " pdb=" C PHE R 50 " pdb=" CB PHE R 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE R 45 " pdb=" CA ILE R 45 " pdb=" CG1 ILE R 45 " pdb=" CG2 ILE R 45 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1338 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP R 88 " 0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C TRP R 88 " -0.079 2.00e-02 2.50e+03 pdb=" O TRP R 88 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR R 89 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 194 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C PHE R 194 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE R 194 " -0.027 2.00e-02 2.50e+03 pdb=" N MET R 195 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 55 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C THR R 55 " -0.058 2.00e-02 2.50e+03 pdb=" O THR R 55 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO R 56 " 0.019 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1141 2.75 - 3.29: 7801 3.29 - 3.83: 12896 3.83 - 4.36: 14793 4.36 - 4.90: 27137 Nonbonded interactions: 63768 Sorted by model distance: nonbonded pdb=" ND2 ASN R 40 " pdb=" OD1 ASP R 68 " model vdw 2.216 3.120 nonbonded pdb=" O GLN S 39 " pdb=" OG1 THR S 116 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.325 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.333 3.120 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.334 3.120 ... (remaining 63763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.280 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.006 0.080 8582 Z= 0.366 Angle : 0.808 15.445 11670 Z= 0.487 Chirality : 0.059 0.598 1341 Planarity : 0.005 0.047 1474 Dihedral : 13.024 80.132 2927 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.93 % Allowed : 1.28 % Favored : 97.79 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.26), residues: 1084 helix: 1.22 (0.27), residues: 377 sheet: 0.20 (0.33), residues: 256 loop : -1.62 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.030 0.002 TYR A 230 PHE 0.018 0.002 PHE R 214 TRP 0.021 0.002 TRP B 339 HIS 0.012 0.002 HIS R 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.37 ( 8580) covalent geometry : angle 0.80814 / 0.49 (11666) SS BOND : bond 0.00686 / 0.35 ( 2) SS BOND : angle 1.48953 / 0.80 ( 4) hydrogen bonds : bond 0.20606 / 13.40 ( 376) hydrogen bonds : angle 6.69945 / 4.84 ( 1077) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.312 Fit side-chains REVERT: A 234 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7431 (tp-100) REVERT: A 238 ASN cc_start: 0.8730 (m110) cc_final: 0.8403 (m110) REVERT: A 323 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7818 (ttm110) REVERT: B 247 ASP cc_start: 0.7774 (t0) cc_final: 0.7573 (t0) REVERT: R 157 MET cc_start: 0.7804 (ttm) cc_final: 0.7443 (ttm) REVERT: R 224 ASN cc_start: 0.7546 (m-40) cc_final: 0.7288 (m110) REVERT: S 18 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7818 (ttm170) outliers start: 8 outliers final: 5 residues processed: 167 average time/residue: 0.1037 time to fit residues: 23.2685 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 54 HIS Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 310 ARG Chi-restraints excluded: chain Y residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.0970 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 204 GLN B 32 GLN R 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112406 restraints weight = 10855.419| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.38 r_work: 0.3158 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8582 Z= 0.142 Angle : 0.594 9.814 11670 Z= 0.313 Chirality : 0.044 0.145 1341 Planarity : 0.004 0.044 1474 Dihedral : 5.845 58.996 1203 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.17 % Allowed : 7.23 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1084 helix: 1.86 (0.27), residues: 374 sheet: 0.30 (0.34), residues: 249 loop : -1.52 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.039 0.002 TYR R 287 PHE 0.019 0.001 PHE A 189 TRP 0.018 0.001 TRP B 339 HIS 0.006 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8580) covalent geometry : angle 0.59354 / 0.31 (11666) SS BOND : bond 0.00752 / 0.38 ( 2) SS BOND : angle 1.18139 / 0.59 ( 4) hydrogen bonds : bond 0.05906 / 3.95 ( 376) hydrogen bonds : angle 4.80629 / 3.41 ( 1077) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 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: 10 poor density : 141 time to evaluate : 0.327 Fit side-chains REVERT: A 24 GLN cc_start: 0.8123 (tt0) cc_final: 0.7829 (mt0) REVERT: A 204 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8239 (mm110) REVERT: A 238 ASN cc_start: 0.8912 (m110) cc_final: 0.8675 (m110) REVERT: R 157 MET cc_start: 0.7918 (ttm) cc_final: 0.7461 (ttm) REVERT: R 270 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7827 (mm) REVERT: S 18 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8327 (tpp-160) REVERT: Y 48 ASP cc_start: 0.8677 (t0) cc_final: 0.8444 (t0) outliers start: 10 outliers final: 6 residues processed: 145 average time/residue: 0.1041 time to fit residues: 20.4218 Evaluate side-chains 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 54 HIS Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 261 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115274 restraints weight = 10685.094| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.33 r_work: 0.3138 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8582 Z= 0.135 Angle : 0.560 11.579 11670 Z= 0.292 Chirality : 0.043 0.153 1341 Planarity : 0.004 0.041 1474 Dihedral : 5.181 53.540 1197 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.52 % Allowed : 11.66 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1084 helix: 2.17 (0.27), residues: 374 sheet: 0.37 (0.33), residues: 264 loop : -1.57 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 323 TYR 0.032 0.002 TYR R 287 PHE 0.016 0.001 PHE A 189 TRP 0.017 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8580) covalent geometry : angle 0.55970 / 0.29 (11666) SS BOND : bond 0.00727 / 0.37 ( 2) SS BOND : angle 1.08859 / 0.56 ( 4) hydrogen bonds : bond 0.05254 / 3.52 ( 376) hydrogen bonds : angle 4.46804 / 3.17 ( 1077) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 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 : 0.348 Fit side-chains REVERT: A 24 GLN cc_start: 0.8177 (tt0) cc_final: 0.7882 (mt0) REVERT: A 204 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8163 (mm110) REVERT: A 238 ASN cc_start: 0.8907 (m110) cc_final: 0.8632 (m110) REVERT: B 75 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8169 (tt0) REVERT: R 54 HIS cc_start: 0.6858 (m170) cc_final: 0.6644 (m170) REVERT: R 157 MET cc_start: 0.7941 (ttm) cc_final: 0.7490 (ttm) outliers start: 13 outliers final: 11 residues processed: 145 average time/residue: 0.0966 time to fit residues: 19.1922 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 62 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 55 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.7506 > 50:) chunk 33 optimal weight: 0.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 261 GLN B 32 GLN R 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113782 restraints weight = 10854.353| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.32 r_work: 0.3118 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8582 Z= 0.150 Angle : 0.570 12.541 11670 Z= 0.296 Chirality : 0.043 0.144 1341 Planarity : 0.004 0.041 1474 Dihedral : 4.695 51.237 1193 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.10 % Allowed : 12.35 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1084 helix: 2.30 (0.27), residues: 370 sheet: 0.44 (0.32), residues: 263 loop : -1.48 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 323 TYR 0.035 0.002 TYR R 287 PHE 0.016 0.001 PHE A 189 TRP 0.014 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8580) covalent geometry : angle 0.57013 / 0.30 (11666) SS BOND : bond 0.00764 / 0.39 ( 2) SS BOND : angle 1.11632 / 0.58 ( 4) hydrogen bonds : bond 0.05367 / 3.60 ( 376) hydrogen bonds : angle 4.43340 / 3.15 ( 1077) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.314 Fit side-chains REVERT: A 24 GLN cc_start: 0.8217 (tt0) cc_final: 0.7854 (mt0) REVERT: A 204 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8178 (mm110) REVERT: A 238 ASN cc_start: 0.8941 (m110) cc_final: 0.8664 (m110) REVERT: A 323 ARG cc_start: 0.8500 (mtp85) cc_final: 0.8218 (mtp180) REVERT: B 75 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8268 (tt0) REVERT: R 54 HIS cc_start: 0.6913 (m170) cc_final: 0.6678 (m170) REVERT: R 157 MET cc_start: 0.7949 (ttm) cc_final: 0.7513 (ttm) REVERT: R 170 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8075 (tt) REVERT: S 18 ARG cc_start: 0.8514 (tpp80) cc_final: 0.7975 (tpt90) REVERT: Y 48 ASP cc_start: 0.8691 (t0) cc_final: 0.8442 (t0) outliers start: 18 outliers final: 12 residues processed: 145 average time/residue: 0.0955 time to fit residues: 19.0603 Evaluate side-chains 145 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 0.0040 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 261 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117422 restraints weight = 10834.850| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.28 r_work: 0.3167 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8582 Z= 0.104 Angle : 0.514 11.210 11670 Z= 0.266 Chirality : 0.041 0.132 1341 Planarity : 0.004 0.038 1474 Dihedral : 4.139 23.402 1191 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.10 % Allowed : 13.40 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1084 helix: 2.53 (0.27), residues: 368 sheet: 0.76 (0.33), residues: 249 loop : -1.49 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 42 TYR 0.018 0.001 TYR A 230 PHE 0.015 0.001 PHE A 189 TRP 0.012 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 8580) covalent geometry : angle 0.51428 / 0.27 (11666) SS BOND : bond 0.00556 / 0.28 ( 2) SS BOND : angle 0.74040 / 0.37 ( 4) hydrogen bonds : bond 0.04342 / 2.94 ( 376) hydrogen bonds : angle 4.21648 / 3.00 ( 1077) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.327 Fit side-chains REVERT: A 24 GLN cc_start: 0.8114 (tt0) cc_final: 0.7809 (mt0) REVERT: A 204 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8177 (mm110) REVERT: A 238 ASN cc_start: 0.8889 (m110) cc_final: 0.8590 (m110) REVERT: B 75 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8124 (tt0) REVERT: R 54 HIS cc_start: 0.6923 (m170) cc_final: 0.6707 (m170) REVERT: R 157 MET cc_start: 0.7944 (ttm) cc_final: 0.7506 (ttm) REVERT: R 170 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7927 (tt) REVERT: S 18 ARG cc_start: 0.8440 (tpp80) cc_final: 0.7920 (tpt90) REVERT: S 83 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6097 (mmt) outliers start: 18 outliers final: 10 residues processed: 149 average time/residue: 0.0892 time to fit residues: 18.4486 Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 190 GLN A 261 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.146810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111434 restraints weight = 10905.088| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.52 r_work: 0.3102 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8582 Z= 0.133 Angle : 0.549 11.645 11670 Z= 0.284 Chirality : 0.042 0.137 1341 Planarity : 0.004 0.039 1474 Dihedral : 4.210 23.140 1191 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.21 % Allowed : 13.64 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1084 helix: 2.51 (0.27), residues: 370 sheet: 0.70 (0.33), residues: 256 loop : -1.39 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 62 TYR 0.028 0.001 TYR R 287 PHE 0.016 0.001 PHE A 189 TRP 0.012 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8580) covalent geometry : angle 0.54836 / 0.28 (11666) SS BOND : bond 0.00691 / 0.35 ( 2) SS BOND : angle 0.98162 / 0.51 ( 4) hydrogen bonds : bond 0.04830 / 3.25 ( 376) hydrogen bonds : angle 4.23642 / 3.02 ( 1077) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 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: 19 poor density : 136 time to evaluate : 0.330 Fit side-chains REVERT: A 24 GLN cc_start: 0.8144 (tt0) cc_final: 0.7839 (mt0) REVERT: A 204 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8189 (mm110) REVERT: A 238 ASN cc_start: 0.8902 (m110) cc_final: 0.8600 (m110) REVERT: B 75 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8167 (tt0) REVERT: R 54 HIS cc_start: 0.7005 (m170) cc_final: 0.6791 (m170) REVERT: R 157 MET cc_start: 0.7982 (ttm) cc_final: 0.7549 (ttm) REVERT: R 170 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7982 (tt) REVERT: S 18 ARG cc_start: 0.8416 (tpp80) cc_final: 0.7890 (tpt90) REVERT: S 83 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6161 (mmt) REVERT: Y 48 ASP cc_start: 0.8672 (t0) cc_final: 0.8376 (t0) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.0926 time to fit residues: 18.9314 Evaluate side-chains 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 190 GLN A 261 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.148197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112870 restraints weight = 11021.764| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.53 r_work: 0.3159 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8582 Z= 0.112 Angle : 0.522 10.490 11670 Z= 0.271 Chirality : 0.041 0.133 1341 Planarity : 0.004 0.038 1474 Dihedral : 4.061 20.118 1191 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.45 % Allowed : 13.40 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1084 helix: 2.62 (0.27), residues: 369 sheet: 0.65 (0.32), residues: 261 loop : -1.35 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 323 TYR 0.026 0.001 TYR R 287 PHE 0.015 0.001 PHE A 189 TRP 0.011 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8580) covalent geometry : angle 0.52165 / 0.27 (11666) SS BOND : bond 0.00585 / 0.30 ( 2) SS BOND : angle 0.81561 / 0.42 ( 4) hydrogen bonds : bond 0.04344 / 2.94 ( 376) hydrogen bonds : angle 4.14293 / 2.94 ( 1077) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 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: 21 poor density : 135 time to evaluate : 0.229 Fit side-chains REVERT: A 24 GLN cc_start: 0.8152 (tt0) cc_final: 0.7840 (mt0) REVERT: A 204 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8196 (mm110) REVERT: A 238 ASN cc_start: 0.8905 (m110) cc_final: 0.8622 (m110) REVERT: A 323 ARG cc_start: 0.8480 (mtp85) cc_final: 0.8195 (mtp180) REVERT: B 75 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8155 (tt0) REVERT: R 157 MET cc_start: 0.8011 (ttm) cc_final: 0.7579 (ttm) REVERT: R 170 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7918 (tt) REVERT: S 18 ARG cc_start: 0.8408 (tpp80) cc_final: 0.7962 (tpt170) REVERT: S 83 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6112 (mmt) REVERT: Y 48 ASP cc_start: 0.8655 (t0) cc_final: 0.8369 (t0) outliers start: 21 outliers final: 12 residues processed: 149 average time/residue: 0.0747 time to fit residues: 15.3043 Evaluate side-chains 145 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116305 restraints weight = 10860.675| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.57 r_work: 0.3157 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8582 Z= 0.111 Angle : 0.519 9.751 11670 Z= 0.270 Chirality : 0.041 0.133 1341 Planarity : 0.004 0.037 1474 Dihedral : 3.990 18.543 1191 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.45 % Allowed : 13.99 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1084 helix: 2.61 (0.27), residues: 369 sheet: 0.68 (0.32), residues: 261 loop : -1.30 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 323 TYR 0.024 0.001 TYR R 287 PHE 0.014 0.001 PHE A 189 TRP 0.010 0.001 TRP B 339 HIS 0.008 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8580) covalent geometry : angle 0.51877 / 0.27 (11666) SS BOND : bond 0.00589 / 0.30 ( 2) SS BOND : angle 0.79015 / 0.41 ( 4) hydrogen bonds : bond 0.04224 / 2.87 ( 376) hydrogen bonds : angle 4.10585 / 2.93 ( 1077) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.256 Fit side-chains REVERT: A 24 GLN cc_start: 0.8119 (tt0) cc_final: 0.7795 (mt0) REVERT: A 204 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8195 (mm110) REVERT: A 238 ASN cc_start: 0.8879 (m110) cc_final: 0.8588 (m110) REVERT: A 323 ARG cc_start: 0.8433 (mtp85) cc_final: 0.8125 (mtp180) REVERT: B 75 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8118 (tt0) REVERT: B 259 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: R 54 HIS cc_start: 0.6814 (m170) cc_final: 0.6582 (m170) REVERT: R 157 MET cc_start: 0.7956 (ttm) cc_final: 0.7523 (ttm) REVERT: S 18 ARG cc_start: 0.8434 (tpp80) cc_final: 0.7999 (tpt170) REVERT: S 83 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6063 (mmt) REVERT: Y 48 ASP cc_start: 0.8666 (t0) cc_final: 0.8339 (t0) REVERT: Y 62 ARG cc_start: 0.7872 (ptt-90) cc_final: 0.7669 (ptt-90) outliers start: 21 outliers final: 17 residues processed: 152 average time/residue: 0.0719 time to fit residues: 15.3794 Evaluate side-chains 154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115543 restraints weight = 10792.023| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.54 r_work: 0.3144 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8582 Z= 0.123 Angle : 0.536 9.672 11670 Z= 0.277 Chirality : 0.042 0.137 1341 Planarity : 0.004 0.040 1474 Dihedral : 4.054 18.814 1191 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.10 % Allowed : 14.69 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1084 helix: 2.54 (0.27), residues: 371 sheet: 0.70 (0.33), residues: 260 loop : -1.26 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 323 TYR 0.022 0.001 TYR R 287 PHE 0.014 0.001 PHE A 189 TRP 0.013 0.001 TRP R 59 HIS 0.008 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8580) covalent geometry : angle 0.53593 / 0.28 (11666) SS BOND : bond 0.00648 / 0.33 ( 2) SS BOND : angle 0.90073 / 0.48 ( 4) hydrogen bonds : bond 0.04474 / 3.03 ( 376) hydrogen bonds : angle 4.16216 / 2.97 ( 1077) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.311 Fit side-chains REVERT: A 24 GLN cc_start: 0.8153 (tt0) cc_final: 0.7831 (mt0) REVERT: A 238 ASN cc_start: 0.8891 (m110) cc_final: 0.8602 (m110) REVERT: A 323 ARG cc_start: 0.8466 (mtp85) cc_final: 0.8159 (mtp180) REVERT: B 75 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8115 (tt0) REVERT: B 259 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: R 157 MET cc_start: 0.7975 (ttm) cc_final: 0.7154 (ttp) REVERT: S 18 ARG cc_start: 0.8394 (tpp80) cc_final: 0.7932 (tpt170) REVERT: S 83 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6136 (mmt) REVERT: Y 48 ASP cc_start: 0.8634 (t0) cc_final: 0.8293 (t0) outliers start: 18 outliers final: 13 residues processed: 151 average time/residue: 0.0879 time to fit residues: 18.1816 Evaluate side-chains 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.146502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112390 restraints weight = 10829.270| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.68 r_work: 0.3107 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8582 Z= 0.142 Angle : 0.563 9.962 11670 Z= 0.292 Chirality : 0.043 0.139 1341 Planarity : 0.004 0.041 1474 Dihedral : 4.177 20.262 1191 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.86 % Allowed : 15.62 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1084 helix: 2.49 (0.27), residues: 371 sheet: 0.77 (0.33), residues: 253 loop : -1.32 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 323 TYR 0.036 0.002 TYR R 287 PHE 0.014 0.001 PHE A 189 TRP 0.016 0.001 TRP R 59 HIS 0.009 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8580) covalent geometry : angle 0.56285 / 0.29 (11666) SS BOND : bond 0.00714 / 0.36 ( 2) SS BOND : angle 0.99525 / 0.53 ( 4) hydrogen bonds : bond 0.04815 / 3.25 ( 376) hydrogen bonds : angle 4.22250 / 3.02 ( 1077) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.318 Fit side-chains REVERT: A 24 GLN cc_start: 0.8205 (tt0) cc_final: 0.7894 (mt0) REVERT: A 238 ASN cc_start: 0.8914 (m110) cc_final: 0.8641 (m110) REVERT: A 323 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8145 (mtp180) REVERT: B 75 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8156 (tt0) REVERT: B 258 ASP cc_start: 0.7655 (t0) cc_final: 0.7366 (t0) REVERT: B 259 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: R 157 MET cc_start: 0.7995 (ttm) cc_final: 0.7174 (ttp) REVERT: S 18 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7925 (tpt170) REVERT: S 83 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6200 (mmt) REVERT: Y 48 ASP cc_start: 0.8649 (t0) cc_final: 0.8289 (t0) REVERT: Y 62 ARG cc_start: 0.7878 (ptt-90) cc_final: 0.7661 (ptt-90) outliers start: 16 outliers final: 13 residues processed: 146 average time/residue: 0.0857 time to fit residues: 17.0118 Evaluate side-chains 151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN B 32 GLN ** R 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116197 restraints weight = 10841.815| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.57 r_work: 0.3195 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8582 Z= 0.100 Angle : 0.517 8.494 11670 Z= 0.266 Chirality : 0.041 0.129 1341 Planarity : 0.003 0.041 1474 Dihedral : 3.908 17.953 1191 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.86 % Allowed : 15.73 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1084 helix: 2.59 (0.27), residues: 369 sheet: 0.85 (0.33), residues: 254 loop : -1.29 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 323 TYR 0.032 0.001 TYR R 287 PHE 0.011 0.001 PHE A 189 TRP 0.009 0.001 TRP S 47 HIS 0.008 0.001 HIS R 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 8580) covalent geometry : angle 0.51686 / 0.27 (11666) SS BOND : bond 0.00487 / 0.25 ( 2) SS BOND : angle 0.66887 / 0.34 ( 4) hydrogen bonds : bond 0.03834 / 2.61 ( 376) hydrogen bonds : angle 4.07144 / 2.91 ( 1077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2409.16 seconds wall clock time: 41 minutes 42.92 seconds (2502.92 seconds total)