Starting phenix.real_space_refine on Fri Jun 6 19:43:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc3_37429/06_2025/8wc3_37429_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc3_37429/06_2025/8wc3_37429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wc3_37429/06_2025/8wc3_37429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc3_37429/06_2025/8wc3_37429.map" model { file = "/net/cci-nas-00/data/ceres_data/8wc3_37429/06_2025/8wc3_37429_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc3_37429/06_2025/8wc3_37429_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5376 2.51 5 N 1427 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8418 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1835 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2491 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "R" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1970 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "S" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1734 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "Y" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 376 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.41, per 1000 atoms: 0.76 Number of scatterers: 8418 At special positions: 0 Unit cell: (117.3, 96.05, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1556 8.00 N 1427 7.00 C 5376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.05 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 36.2% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.925A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.595A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.040A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.659A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.832A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 4.107A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.881A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 50 removed outlier: 4.033A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 44 " --> pdb=" O ASN R 40 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE R 50 " --> pdb=" O SER R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 74 removed outlier: 3.511A pdb=" N TRP R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY R 72 " --> pdb=" O ASP R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 85 removed outlier: 3.528A pdb=" N CYS R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG R 82 " --> pdb=" O CYS R 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 126 removed outlier: 3.755A pdb=" N CYS R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER R 100 " --> pdb=" O LYS R 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 105 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 135 through 160 Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 174 removed outlier: 3.565A pdb=" N GLN R 174 " --> pdb=" O LEU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 221 removed outlier: 3.798A pdb=" N LEU R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) Proline residue: R 201 - end of helix removed outlier: 3.619A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG R 221 " --> pdb=" O LYS R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 275 Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 301 removed outlier: 4.938A pdb=" N ASN R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER R 294 " --> pdb=" O GLY R 290 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix removed outlier: 3.556A pdb=" N TYR R 301 " --> pdb=" O ASN R 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.186A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 24 removed outlier: 3.509A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.919A pdb=" N ALA Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET Y 38 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.755A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.534A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.519A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.841A 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: 6.907A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.917A 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: 6.965A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.645A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.699A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.648A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.648A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.791A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 369 hydrogen bonds defined for protein. 1047 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: 2.97 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1367 1.31 - 1.44: 2457 1.44 - 1.57: 4698 1.57 - 1.70: 1 1.70 - 1.84: 85 Bond restraints: 8608 Sorted by residual: bond pdb=" C LEU R 74 " pdb=" O LEU R 74 " ideal model delta sigma weight residual 1.234 1.188 0.046 8.30e-03 1.45e+04 3.05e+01 bond pdb=" N ILE R 103 " pdb=" CA ILE R 103 " ideal model delta sigma weight residual 1.460 1.395 0.065 1.32e-02 5.74e+03 2.42e+01 bond pdb=" CA LEU Y 15 " pdb=" C LEU Y 15 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.36e-02 5.41e+03 2.29e+01 bond pdb=" CA ILE R 75 " pdb=" CB ILE R 75 " ideal model delta sigma weight residual 1.540 1.480 0.059 1.29e-02 6.01e+03 2.10e+01 bond pdb=" CA GLN A 24 " pdb=" C GLN A 24 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.29e-02 6.01e+03 2.00e+01 ... (remaining 8603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 11357 2.46 - 4.93: 291 4.93 - 7.39: 46 7.39 - 9.86: 17 9.86 - 12.32: 7 Bond angle restraints: 11718 Sorted by residual: angle pdb=" N LYS Y 14 " pdb=" CA LYS Y 14 " pdb=" C LYS Y 14 " ideal model delta sigma weight residual 111.36 123.27 -11.91 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N ILE R 75 " pdb=" CA ILE R 75 " pdb=" C ILE R 75 " ideal model delta sigma weight residual 110.72 120.96 -10.24 1.01e+00 9.80e-01 1.03e+02 angle pdb=" N ALA Y 10 " pdb=" CA ALA Y 10 " pdb=" C ALA Y 10 " ideal model delta sigma weight residual 112.12 124.44 -12.32 1.34e+00 5.57e-01 8.46e+01 angle pdb=" N ALA Y 12 " pdb=" CA ALA Y 12 " pdb=" C ALA Y 12 " ideal model delta sigma weight residual 111.71 102.47 9.24 1.15e+00 7.56e-01 6.45e+01 angle pdb=" N THR S 238 " pdb=" CA THR S 238 " pdb=" C THR S 238 " ideal model delta sigma weight residual 109.96 120.60 -10.64 1.50e+00 4.44e-01 5.03e+01 ... (remaining 11713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4491 16.03 - 32.05: 414 32.05 - 48.08: 104 48.08 - 64.10: 23 64.10 - 80.13: 9 Dihedral angle restraints: 5041 sinusoidal: 1795 harmonic: 3246 Sorted by residual: dihedral pdb=" C TYR S 235 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " ideal model delta harmonic sigma weight residual -122.60 -150.56 27.96 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " ideal model delta harmonic sigma weight residual 122.80 149.53 -26.73 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 43.24 49.76 1 1.00e+01 1.00e-02 3.40e+01 ... (remaining 5038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 1333 0.231 - 0.461: 16 0.461 - 0.692: 0 0.692 - 0.922: 0 0.922 - 1.153: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.32e+01 chirality pdb=" CA ILE R 75 " pdb=" N ILE R 75 " pdb=" C ILE R 75 " pdb=" CB ILE R 75 " both_signs ideal model delta sigma weight residual False 2.43 2.00 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ALA Y 10 " pdb=" N ALA Y 10 " pdb=" C ALA Y 10 " pdb=" CB ALA Y 10 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 1347 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 75 " 0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ILE R 75 " -0.072 2.00e-02 2.50e+03 pdb=" O ILE R 75 " 0.027 2.00e-02 2.50e+03 pdb=" N MET R 76 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 217 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS R 217 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS R 217 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY R 218 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 285 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.03e+00 pdb=" C TYR A 285 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR A 285 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 286 " 0.017 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.06: 2 2.06 - 2.77: 1615 2.77 - 3.48: 11105 3.48 - 4.19: 18842 4.19 - 4.90: 33918 Nonbonded interactions: 65482 Sorted by model distance: nonbonded pdb=" NH1 ARG A 352 " pdb=" O ILE R 223 " model vdw 1.356 3.120 nonbonded pdb=" OG SER R 100 " pdb=" CG2 ILE R 158 " model vdw 1.809 3.460 nonbonded pdb=" OG SER B 281 " pdb=" O HIS Y 44 " model vdw 2.232 3.040 nonbonded pdb=" N GLN R 52 " pdb=" OE1 GLN R 52 " model vdw 2.246 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.260 3.040 ... (remaining 65477 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: 0.720 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 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 0.065 8611 Z= 0.457 Angle : 0.957 12.323 11724 Z= 0.638 Chirality : 0.071 1.153 1350 Planarity : 0.005 0.049 1484 Dihedral : 13.967 80.127 2938 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.40 % Allowed : 2.68 % Favored : 95.93 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.25), residues: 1099 helix: 0.21 (0.28), residues: 348 sheet: 0.08 (0.33), residues: 276 loop : -1.91 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 261 HIS 0.003 0.001 HIS B 183 PHE 0.017 0.001 PHE R 289 TYR 0.026 0.001 TYR S 235 ARG 0.007 0.000 ARG R 309 Details of bonding type rmsd hydrogen bonds : bond 0.21951 ( 369) hydrogen bonds : angle 7.58189 ( 1047) SS BOND : bond 0.01405 ( 3) SS BOND : angle 2.97041 ( 6) covalent geometry : bond 0.00646 ( 8608) covalent geometry : angle 0.95513 (11718) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.839 Fit side-chains REVERT: S 235 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.5976 (t80) outliers start: 12 outliers final: 4 residues processed: 152 average time/residue: 1.0835 time to fit residues: 176.2179 Evaluate side-chains 100 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 309 ARG Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 261 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144780 restraints weight = 10361.457| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.99 r_work: 0.3462 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8611 Z= 0.154 Angle : 0.608 8.040 11724 Z= 0.320 Chirality : 0.044 0.275 1350 Planarity : 0.004 0.049 1484 Dihedral : 5.179 49.038 1224 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.26 % Allowed : 13.39 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.26), residues: 1099 helix: 1.75 (0.28), residues: 352 sheet: 0.14 (0.33), residues: 276 loop : -1.58 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.014 0.002 PHE B 151 TYR 0.034 0.002 TYR S 235 ARG 0.008 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.05730 ( 369) hydrogen bonds : angle 4.91770 ( 1047) SS BOND : bond 0.00559 ( 3) SS BOND : angle 1.34874 ( 6) covalent geometry : bond 0.00345 ( 8608) covalent geometry : angle 0.60771 (11718) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.880 Fit side-chains REVERT: R 167 VAL cc_start: 0.7276 (OUTLIER) cc_final: 0.6782 (p) REVERT: R 294 SER cc_start: 0.8393 (t) cc_final: 0.8019 (m) REVERT: S 93 MET cc_start: 0.7388 (mpp) cc_final: 0.6415 (mtp) outliers start: 28 outliers final: 17 residues processed: 117 average time/residue: 1.0921 time to fit residues: 137.1982 Evaluate side-chains 105 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 83 optimal weight: 0.0870 chunk 53 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.176632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143850 restraints weight = 10419.561| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.06 r_work: 0.3443 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8611 Z= 0.140 Angle : 0.572 7.432 11724 Z= 0.300 Chirality : 0.042 0.251 1350 Planarity : 0.004 0.046 1484 Dihedral : 4.570 44.954 1217 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.26 % Allowed : 16.18 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1099 helix: 2.07 (0.28), residues: 351 sheet: 0.17 (0.33), residues: 276 loop : -1.53 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE B 151 TYR 0.033 0.002 TYR S 235 ARG 0.012 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.05283 ( 369) hydrogen bonds : angle 4.64144 ( 1047) SS BOND : bond 0.00555 ( 3) SS BOND : angle 1.01535 ( 6) covalent geometry : bond 0.00318 ( 8608) covalent geometry : angle 0.57154 (11718) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.909 Fit side-chains REVERT: B 325 MET cc_start: 0.7300 (ttm) cc_final: 0.7030 (tpt) REVERT: S 93 MET cc_start: 0.7423 (mpp) cc_final: 0.6490 (mtp) REVERT: S 235 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.6399 (t80) outliers start: 28 outliers final: 17 residues processed: 118 average time/residue: 1.0543 time to fit residues: 133.6290 Evaluate side-chains 109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 0.0020 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.179530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147675 restraints weight = 10446.227| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.02 r_work: 0.3491 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8611 Z= 0.104 Angle : 0.517 6.528 11724 Z= 0.269 Chirality : 0.041 0.209 1350 Planarity : 0.004 0.045 1484 Dihedral : 4.227 43.272 1215 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.21 % Allowed : 18.98 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.26), residues: 1099 helix: 2.29 (0.28), residues: 349 sheet: 0.30 (0.33), residues: 276 loop : -1.44 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.027 0.001 TYR S 235 ARG 0.011 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 369) hydrogen bonds : angle 4.30364 ( 1047) SS BOND : bond 0.00438 ( 3) SS BOND : angle 0.76781 ( 6) covalent geometry : bond 0.00224 ( 8608) covalent geometry : angle 0.51674 (11718) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.836 Fit side-chains REVERT: B 325 MET cc_start: 0.7142 (ttm) cc_final: 0.6896 (tpt) REVERT: R 294 SER cc_start: 0.8489 (t) cc_final: 0.8172 (t) REVERT: S 93 MET cc_start: 0.7380 (mpp) cc_final: 0.6409 (mtp) outliers start: 19 outliers final: 9 residues processed: 112 average time/residue: 1.1324 time to fit residues: 135.9254 Evaluate side-chains 102 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.174387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142629 restraints weight = 10387.920| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.95 r_work: 0.3431 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8611 Z= 0.169 Angle : 0.608 10.567 11724 Z= 0.318 Chirality : 0.043 0.228 1350 Planarity : 0.004 0.047 1484 Dihedral : 4.573 45.677 1215 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.31 % Allowed : 18.63 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.26), residues: 1099 helix: 1.97 (0.28), residues: 353 sheet: 0.20 (0.33), residues: 279 loop : -1.54 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 63 HIS 0.004 0.001 HIS S 167 PHE 0.015 0.002 PHE B 151 TYR 0.032 0.002 TYR S 235 ARG 0.011 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.05685 ( 369) hydrogen bonds : angle 4.56757 ( 1047) SS BOND : bond 0.00646 ( 3) SS BOND : angle 0.97808 ( 6) covalent geometry : bond 0.00396 ( 8608) covalent geometry : angle 0.60763 (11718) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.826 Fit side-chains REVERT: A 359 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: B 234 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7012 (t80) REVERT: B 325 MET cc_start: 0.7417 (ttm) cc_final: 0.7127 (tpt) REVERT: R 33 ILE cc_start: 0.8313 (tt) cc_final: 0.8079 (mt) outliers start: 37 outliers final: 24 residues processed: 119 average time/residue: 1.0462 time to fit residues: 133.8037 Evaluate side-chains 117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143209 restraints weight = 10330.544| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.93 r_work: 0.3446 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8611 Z= 0.138 Angle : 0.583 9.225 11724 Z= 0.302 Chirality : 0.042 0.207 1350 Planarity : 0.004 0.053 1484 Dihedral : 4.490 46.748 1215 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.07 % Allowed : 19.56 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.26), residues: 1099 helix: 2.11 (0.28), residues: 352 sheet: 0.22 (0.33), residues: 277 loop : -1.53 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 151 TYR 0.030 0.001 TYR S 235 ARG 0.014 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 369) hydrogen bonds : angle 4.40604 ( 1047) SS BOND : bond 0.00545 ( 3) SS BOND : angle 0.83614 ( 6) covalent geometry : bond 0.00317 ( 8608) covalent geometry : angle 0.58293 (11718) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.930 Fit side-chains REVERT: A 359 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: B 286 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7316 (pp) REVERT: B 325 MET cc_start: 0.7327 (ttm) cc_final: 0.7071 (tpt) REVERT: R 167 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6655 (p) REVERT: R 294 SER cc_start: 0.8616 (t) cc_final: 0.8122 (m) REVERT: S 93 MET cc_start: 0.7510 (mtp) cc_final: 0.6469 (mtp) outliers start: 35 outliers final: 24 residues processed: 118 average time/residue: 1.0129 time to fit residues: 128.9128 Evaluate side-chains 118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.172926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141121 restraints weight = 10481.833| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.98 r_work: 0.3407 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8611 Z= 0.199 Angle : 0.654 9.109 11724 Z= 0.345 Chirality : 0.045 0.227 1350 Planarity : 0.005 0.060 1484 Dihedral : 4.809 48.359 1215 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.42 % Allowed : 19.21 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1099 helix: 1.87 (0.28), residues: 353 sheet: 0.10 (0.33), residues: 279 loop : -1.62 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.004 0.001 HIS S 167 PHE 0.017 0.002 PHE B 151 TYR 0.031 0.002 TYR S 235 ARG 0.016 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.06214 ( 369) hydrogen bonds : angle 4.70540 ( 1047) SS BOND : bond 0.00688 ( 3) SS BOND : angle 1.03798 ( 6) covalent geometry : bond 0.00473 ( 8608) covalent geometry : angle 0.65351 (11718) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.857 Fit side-chains REVERT: A 20 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 359 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: B 234 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7068 (t80) REVERT: B 286 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7153 (pp) REVERT: B 325 MET cc_start: 0.7542 (ttm) cc_final: 0.7249 (tpt) REVERT: R 167 VAL cc_start: 0.7172 (OUTLIER) cc_final: 0.6678 (p) REVERT: S 93 MET cc_start: 0.7484 (mtp) cc_final: 0.6443 (mtp) outliers start: 38 outliers final: 27 residues processed: 116 average time/residue: 1.2953 time to fit residues: 161.3415 Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 30.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.176343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144106 restraints weight = 10510.401| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.98 r_work: 0.3459 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8611 Z= 0.126 Angle : 0.579 9.045 11724 Z= 0.301 Chirality : 0.042 0.182 1350 Planarity : 0.004 0.069 1484 Dihedral : 4.509 48.684 1215 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.49 % Allowed : 20.49 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.26), residues: 1099 helix: 2.13 (0.28), residues: 353 sheet: 0.19 (0.33), residues: 277 loop : -1.50 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.026 0.001 TYR S 235 ARG 0.018 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 369) hydrogen bonds : angle 4.38646 ( 1047) SS BOND : bond 0.00502 ( 3) SS BOND : angle 0.78273 ( 6) covalent geometry : bond 0.00281 ( 8608) covalent geometry : angle 0.57905 (11718) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.860 Fit side-chains REVERT: A 20 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 359 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: B 234 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7022 (t80) REVERT: B 325 MET cc_start: 0.7358 (ttm) cc_final: 0.7150 (tpt) REVERT: R 167 VAL cc_start: 0.7155 (OUTLIER) cc_final: 0.6656 (p) REVERT: R 294 SER cc_start: 0.8607 (t) cc_final: 0.8278 (t) REVERT: S 93 MET cc_start: 0.7459 (mtp) cc_final: 0.6429 (mtp) REVERT: S 160 ARG cc_start: 0.7291 (ttm-80) cc_final: 0.6967 (ttp-110) outliers start: 30 outliers final: 24 residues processed: 113 average time/residue: 1.0385 time to fit residues: 126.4702 Evaluate side-chains 115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140862 restraints weight = 10517.681| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.99 r_work: 0.3406 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8611 Z= 0.199 Angle : 0.659 8.641 11724 Z= 0.346 Chirality : 0.044 0.218 1350 Planarity : 0.005 0.070 1484 Dihedral : 4.802 49.315 1215 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.61 % Allowed : 20.72 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1099 helix: 1.87 (0.28), residues: 353 sheet: 0.10 (0.33), residues: 279 loop : -1.61 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.002 PHE B 151 TYR 0.032 0.002 TYR S 235 ARG 0.018 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.06120 ( 369) hydrogen bonds : angle 4.70057 ( 1047) SS BOND : bond 0.00675 ( 3) SS BOND : angle 1.02200 ( 6) covalent geometry : bond 0.00477 ( 8608) covalent geometry : angle 0.65838 (11718) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.654 Fit side-chains REVERT: B 32 GLN cc_start: 0.7644 (mt0) cc_final: 0.7135 (pt0) REVERT: B 175 GLN cc_start: 0.8340 (mp10) cc_final: 0.7854 (mp10) REVERT: B 234 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7058 (t80) REVERT: B 325 MET cc_start: 0.7539 (ttm) cc_final: 0.7265 (tpt) REVERT: R 167 VAL cc_start: 0.7285 (OUTLIER) cc_final: 0.6763 (p) outliers start: 31 outliers final: 26 residues processed: 111 average time/residue: 1.2627 time to fit residues: 152.0218 Evaluate side-chains 120 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.174067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141403 restraints weight = 10362.325| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.98 r_work: 0.3427 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8611 Z= 0.167 Angle : 0.631 9.045 11724 Z= 0.330 Chirality : 0.043 0.222 1350 Planarity : 0.005 0.073 1484 Dihedral : 4.739 50.078 1215 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.61 % Allowed : 20.95 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1099 helix: 1.91 (0.28), residues: 353 sheet: 0.11 (0.33), residues: 279 loop : -1.59 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.002 PHE B 151 TYR 0.030 0.002 TYR S 235 ARG 0.019 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.05548 ( 369) hydrogen bonds : angle 4.62296 ( 1047) SS BOND : bond 0.00606 ( 3) SS BOND : angle 0.91206 ( 6) covalent geometry : bond 0.00393 ( 8608) covalent geometry : angle 0.63123 (11718) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.858 Fit side-chains REVERT: A 20 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7561 (mt-10) REVERT: B 32 GLN cc_start: 0.7624 (mt0) cc_final: 0.7157 (pt0) REVERT: B 234 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7019 (t80) REVERT: B 325 MET cc_start: 0.7483 (ttm) cc_final: 0.7246 (tpt) REVERT: R 167 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6737 (p) REVERT: S 93 MET cc_start: 0.7505 (mtp) cc_final: 0.6450 (mtp) REVERT: S 160 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6970 (ttp-110) outliers start: 31 outliers final: 27 residues processed: 110 average time/residue: 1.0297 time to fit residues: 121.8305 Evaluate side-chains 119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.176405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144065 restraints weight = 10612.016| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.97 r_work: 0.3460 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8611 Z= 0.126 Angle : 0.586 9.217 11724 Z= 0.304 Chirality : 0.042 0.192 1350 Planarity : 0.004 0.076 1484 Dihedral : 4.497 49.152 1215 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.38 % Allowed : 20.95 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.26), residues: 1099 helix: 2.10 (0.29), residues: 353 sheet: 0.31 (0.34), residues: 264 loop : -1.51 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.027 0.001 TYR S 235 ARG 0.018 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 369) hydrogen bonds : angle 4.38315 ( 1047) SS BOND : bond 0.00510 ( 3) SS BOND : angle 0.78331 ( 6) covalent geometry : bond 0.00285 ( 8608) covalent geometry : angle 0.58610 (11718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6535.47 seconds wall clock time: 113 minutes 38.29 seconds (6818.29 seconds total)