Starting phenix.real_space_refine on Fri Aug 22 22:23:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihj_35446/08_2025/8ihj_35446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihj_35446/08_2025/8ihj_35446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihj_35446/08_2025/8ihj_35446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihj_35446/08_2025/8ihj_35446.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihj_35446/08_2025/8ihj_35446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihj_35446/08_2025/8ihj_35446.cif" } resolution = 3.07 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= 0.004 sd= 0.049 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 53 5.16 5 C 5450 2.51 5 N 1435 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8509 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 273} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1702 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1701 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2480 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'P9X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.23 Number of scatterers: 8509 At special positions: 0 Unit cell: (93.6, 116.22, 132.6, 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 53 16.00 O 1571 8.00 N 1435 7.00 C 5450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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: 0.68 Conformation dependent library (CDL) restraints added in 442.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.6% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 23 through 28 removed outlier: 3.705A pdb=" N ALA R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 55 removed outlier: 3.513A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.613A pdb=" N VAL R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 127 removed outlier: 3.515A pdb=" N LEU R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA R 108 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 138 removed outlier: 3.729A pdb=" N ASN R 137 " --> pdb=" O HIS R 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS R 138 " --> pdb=" O ALA R 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 134 through 138' Processing helix chain 'R' and resid 140 through 158 removed outlier: 3.835A pdb=" N VAL R 156 " --> pdb=" O TRP R 152 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY R 157 " --> pdb=" O GLY R 153 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 165 removed outlier: 4.024A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS R 165 " --> pdb=" O HIS R 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 160 through 165' Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.910A pdb=" N PHE R 193 " --> pdb=" O HIS R 189 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.600A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 260 removed outlier: 3.744A pdb=" N ALA R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.590A pdb=" N VAL R 250 " --> pdb=" O PRO R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 280 removed outlier: 4.239A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 294 removed outlier: 3.951A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.753A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.628A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.149A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.576A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.766A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.769A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.823A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.990A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.619A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.727A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.690A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.833A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.521A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.542A pdb=" N ILE R 169 " --> pdb=" O VAL R 176 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 174 " --> pdb=" O ASN R 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 9.442A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.716A pdb=" N SER S 7 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 58 through 60 Processing sheet with id=AA5, first strand: chain 'S' and resid 45 through 46 removed outlier: 3.502A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.500A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.571A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.516A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.561A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.776A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.979A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.565A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.505A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.062A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1053 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: 0.88 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2734 1.34 - 1.46: 2178 1.46 - 1.58: 3720 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 8703 Sorted by residual: bond pdb=" C5 P9X R 501 " pdb=" O2 P9X R 501 " ideal model delta sigma weight residual 1.250 1.306 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C4 P9X R 501 " pdb=" C5 P9X R 501 " ideal model delta sigma weight residual 1.530 1.481 0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" CG PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.69e+00 bond pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.56e+00 bond pdb=" C5 P9X R 501 " pdb=" O3 P9X R 501 " ideal model delta sigma weight residual 1.248 1.224 0.024 2.00e-02 2.50e+03 1.49e+00 ... (remaining 8698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 11613 1.36 - 2.72: 170 2.72 - 4.08: 33 4.08 - 5.44: 14 5.44 - 6.80: 7 Bond angle restraints: 11837 Sorted by residual: angle pdb=" CA GLN A 333 " pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 107.55 4.45 1.40e+00 5.10e-01 1.01e+01 angle pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " pdb=" CD GLN A 333 " ideal model delta sigma weight residual 112.60 117.41 -4.81 1.70e+00 3.46e-01 8.00e+00 angle pdb=" CA ASP S 201 " pdb=" C ASP S 201 " pdb=" N ARG S 202 " ideal model delta sigma weight residual 118.59 122.38 -3.79 1.63e+00 3.76e-01 5.40e+00 angle pdb=" C4 P9X R 501 " pdb=" C5 P9X R 501 " pdb=" O3 P9X R 501 " ideal model delta sigma weight residual 116.38 121.98 -5.60 3.00e+00 1.11e-01 3.48e+00 ... (remaining 11832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4401 18.01 - 36.02: 534 36.02 - 54.04: 116 54.04 - 72.05: 24 72.05 - 90.06: 9 Dihedral angle restraints: 5084 sinusoidal: 1832 harmonic: 3252 Sorted by residual: dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " pdb=" OD1 ASP B 195 " ideal model delta sinusoidal sigma weight residual -30.00 -90.12 60.12 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual -86.00 -114.57 28.57 1 1.00e+01 1.00e-02 1.17e+01 ... (remaining 5081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 831 0.027 - 0.054: 317 0.054 - 0.081: 126 0.081 - 0.108: 52 0.108 - 0.135: 32 Chirality restraints: 1358 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE R 178 " pdb=" N ILE R 178 " pdb=" C ILE R 178 " pdb=" CB ILE R 178 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL S 147 " pdb=" N VAL S 147 " pdb=" C VAL S 147 " pdb=" CB VAL S 147 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1355 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO S 75 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 98 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO R 99 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 99 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 99 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO S 236 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.027 5.00e-02 4.00e+02 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 248 2.70 - 3.25: 8082 3.25 - 3.80: 12738 3.80 - 4.35: 16676 4.35 - 4.90: 28903 Nonbonded interactions: 66647 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.193 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.217 3.040 nonbonded pdb=" O ILE S 138 " pdb=" OG1 THR S 238 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASN R 68 " pdb=" OG SER R 148 " model vdw 2.289 3.040 ... (remaining 66642 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: 0.530 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.000 Find NCS groups from input model: 0.100 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 0.002 0.056 8706 Z= 0.103 Angle : 0.475 6.803 11843 Z= 0.248 Chirality : 0.039 0.135 1358 Planarity : 0.005 0.112 1499 Dihedral : 16.684 90.058 2973 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.11 % Allowed : 27.10 % Favored : 72.79 % 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 aren not related in a simple way. whole: -0.90 (0.25), residues: 1106 helix: -0.25 (0.28), residues: 350 sheet: -0.09 (0.33), residues: 263 loop : -1.04 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 160 TYR 0.020 0.001 TYR S 235 PHE 0.018 0.001 PHE R 107 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8703) covalent geometry : angle 0.47462 (11837) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.68988 ( 6) hydrogen bonds : bond 0.28286 ( 372) hydrogen bonds : angle 8.23622 ( 1053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.316 Fit side-chains REVERT: A 271 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7979 (ptmm) REVERT: A 313 ARG cc_start: 0.6520 (mtp180) cc_final: 0.5855 (ptp-170) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.0985 time to fit residues: 16.3000 Evaluate side-chains 117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.159589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106775 restraints weight = 11036.210| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.79 r_work: 0.3185 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8706 Z= 0.124 Angle : 0.511 8.866 11843 Z= 0.275 Chirality : 0.042 0.156 1358 Planarity : 0.004 0.070 1499 Dihedral : 4.903 52.035 1221 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.56 % Allowed : 24.23 % Favored : 72.22 % 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 aren not related in a simple way. whole: -0.39 (0.25), residues: 1106 helix: 0.66 (0.27), residues: 364 sheet: 0.06 (0.32), residues: 265 loop : -1.11 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.020 0.001 TYR S 235 PHE 0.011 0.001 PHE S 27 TRP 0.022 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8703) covalent geometry : angle 0.51082 (11837) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.93426 ( 6) hydrogen bonds : bond 0.05057 ( 372) hydrogen bonds : angle 5.05987 ( 1053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.343 Fit side-chains REVERT: R 255 PHE cc_start: 0.7905 (t80) cc_final: 0.7693 (t80) REVERT: A 272 ASP cc_start: 0.8094 (m-30) cc_final: 0.7831 (m-30) REVERT: A 313 ARG cc_start: 0.6669 (mtp180) cc_final: 0.5733 (ptp-170) REVERT: S 93 MET cc_start: 0.7940 (ttt) cc_final: 0.7692 (ttt) REVERT: S 202 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7440 (mtm-85) REVERT: S 235 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6224 (t80) outliers start: 31 outliers final: 10 residues processed: 159 average time/residue: 0.0804 time to fit residues: 17.8695 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 184 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.155879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102448 restraints weight = 11054.048| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.79 r_work: 0.3131 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8706 Z= 0.210 Angle : 0.568 9.917 11843 Z= 0.301 Chirality : 0.044 0.207 1358 Planarity : 0.004 0.058 1499 Dihedral : 5.044 49.594 1221 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.59 % Allowed : 23.65 % Favored : 71.76 % 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 aren not related in a simple way. whole: -0.35 (0.25), residues: 1106 helix: 1.00 (0.28), residues: 363 sheet: 0.03 (0.31), residues: 266 loop : -1.34 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.024 0.002 TYR S 235 PHE 0.018 0.001 PHE S 27 TRP 0.022 0.001 TRP B 82 HIS 0.004 0.001 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 8703) covalent geometry : angle 0.56712 (11837) SS BOND : bond 0.00160 ( 3) SS BOND : angle 1.11146 ( 6) hydrogen bonds : bond 0.05075 ( 372) hydrogen bonds : angle 4.80690 ( 1053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.196 Fit side-chains REVERT: R 45 ASN cc_start: 0.8031 (m-40) cc_final: 0.7505 (m110) REVERT: R 277 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7066 (t80) REVERT: A 272 ASP cc_start: 0.8111 (m-30) cc_final: 0.7858 (m-30) REVERT: S 93 MET cc_start: 0.7986 (ttt) cc_final: 0.7715 (ttt) REVERT: S 235 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.6385 (t80) REVERT: B 234 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8600 (t80) REVERT: C 37 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7924 (tt) outliers start: 40 outliers final: 21 residues processed: 156 average time/residue: 0.0757 time to fit residues: 16.6321 Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 0.0770 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.161201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108176 restraints weight = 11151.395| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.88 r_work: 0.3212 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8706 Z= 0.093 Angle : 0.468 9.163 11843 Z= 0.247 Chirality : 0.040 0.133 1358 Planarity : 0.004 0.052 1499 Dihedral : 4.376 37.625 1221 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.56 % Allowed : 24.34 % Favored : 72.10 % 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 aren not related in a simple way. whole: -0.06 (0.25), residues: 1106 helix: 1.36 (0.29), residues: 365 sheet: -0.01 (0.31), residues: 266 loop : -1.14 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.018 0.001 TYR S 235 PHE 0.011 0.001 PHE R 38 TRP 0.022 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 8703) covalent geometry : angle 0.46765 (11837) SS BOND : bond 0.00245 ( 3) SS BOND : angle 0.96837 ( 6) hydrogen bonds : bond 0.03506 ( 372) hydrogen bonds : angle 4.35271 ( 1053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.301 Fit side-chains REVERT: R 45 ASN cc_start: 0.7963 (m-40) cc_final: 0.7616 (m110) REVERT: R 192 MET cc_start: 0.5887 (tmm) cc_final: 0.5526 (tpp) REVERT: R 277 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.7051 (t80) REVERT: A 272 ASP cc_start: 0.8180 (m-30) cc_final: 0.7940 (m-30) REVERT: A 309 ASP cc_start: 0.7741 (t0) cc_final: 0.7514 (t0) REVERT: A 313 ARG cc_start: 0.6745 (mtp180) cc_final: 0.5726 (ptp-170) REVERT: A 318 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6171 (tm-30) REVERT: S 93 MET cc_start: 0.7938 (ttt) cc_final: 0.7635 (ttt) REVERT: S 202 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7225 (mtm-85) REVERT: S 235 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.5888 (t80) REVERT: B 234 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8601 (t80) outliers start: 31 outliers final: 14 residues processed: 155 average time/residue: 0.0764 time to fit residues: 16.7720 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103288 restraints weight = 11088.062| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.86 r_work: 0.3143 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8706 Z= 0.179 Angle : 0.532 10.955 11843 Z= 0.281 Chirality : 0.043 0.177 1358 Planarity : 0.004 0.055 1499 Dihedral : 4.763 45.240 1221 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.36 % Allowed : 24.00 % Favored : 71.64 % 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 aren not related in a simple way. whole: -0.09 (0.25), residues: 1106 helix: 1.33 (0.28), residues: 365 sheet: 0.07 (0.31), residues: 266 loop : -1.23 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 160 TYR 0.021 0.001 TYR S 235 PHE 0.015 0.001 PHE S 27 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8703) covalent geometry : angle 0.53225 (11837) SS BOND : bond 0.00098 ( 3) SS BOND : angle 0.81978 ( 6) hydrogen bonds : bond 0.04183 ( 372) hydrogen bonds : angle 4.43374 ( 1053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.233 Fit side-chains REVERT: R 38 PHE cc_start: 0.7826 (t80) cc_final: 0.7602 (t80) REVERT: R 45 ASN cc_start: 0.7980 (m-40) cc_final: 0.7750 (m110) REVERT: R 277 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6942 (t80) REVERT: A 272 ASP cc_start: 0.8167 (m-30) cc_final: 0.7929 (m-30) REVERT: A 309 ASP cc_start: 0.7748 (t0) cc_final: 0.7519 (t0) REVERT: A 313 ARG cc_start: 0.6798 (mtp180) cc_final: 0.5754 (ptp-170) REVERT: A 318 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6234 (tm-30) REVERT: S 93 MET cc_start: 0.7977 (ttt) cc_final: 0.7738 (ttt) REVERT: S 223 ASP cc_start: 0.7942 (m-30) cc_final: 0.7727 (m-30) REVERT: S 235 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.6280 (t80) REVERT: S 237 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7162 (pp) REVERT: B 234 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8649 (t80) outliers start: 38 outliers final: 29 residues processed: 153 average time/residue: 0.0826 time to fit residues: 17.4909 Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 24 optimal weight: 0.0980 chunk 75 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 ASN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101670 restraints weight = 11087.249| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.76 r_work: 0.3126 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8706 Z= 0.229 Angle : 0.578 11.373 11843 Z= 0.304 Chirality : 0.044 0.215 1358 Planarity : 0.004 0.054 1499 Dihedral : 4.951 46.532 1221 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.40 % Allowed : 23.65 % Favored : 70.95 % 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 aren not related in a simple way. whole: -0.30 (0.25), residues: 1106 helix: 1.12 (0.28), residues: 367 sheet: -0.04 (0.31), residues: 265 loop : -1.34 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 160 TYR 0.026 0.002 TYR S 235 PHE 0.019 0.002 PHE S 27 TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 8703) covalent geometry : angle 0.57752 (11837) SS BOND : bond 0.00129 ( 3) SS BOND : angle 0.90855 ( 6) hydrogen bonds : bond 0.04556 ( 372) hydrogen bonds : angle 4.54374 ( 1053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.367 Fit side-chains REVERT: R 277 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6954 (t80) REVERT: A 309 ASP cc_start: 0.7821 (t0) cc_final: 0.7547 (t0) REVERT: A 318 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: S 93 MET cc_start: 0.7988 (ttt) cc_final: 0.7732 (ttt) REVERT: S 235 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.6257 (t80) REVERT: B 234 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8610 (t80) outliers start: 47 outliers final: 36 residues processed: 157 average time/residue: 0.0959 time to fit residues: 21.0438 Evaluate side-chains 157 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.156912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.103750 restraints weight = 11176.060| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.79 r_work: 0.3151 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8706 Z= 0.155 Angle : 0.526 11.234 11843 Z= 0.276 Chirality : 0.042 0.177 1358 Planarity : 0.004 0.053 1499 Dihedral : 4.650 44.708 1221 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.05 % Allowed : 24.80 % Favored : 70.15 % 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 aren not related in a simple way. whole: -0.20 (0.25), residues: 1106 helix: 1.25 (0.28), residues: 367 sheet: -0.03 (0.31), residues: 260 loop : -1.28 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 160 TYR 0.022 0.001 TYR S 235 PHE 0.022 0.001 PHE R 276 TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8703) covalent geometry : angle 0.52615 (11837) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.84329 ( 6) hydrogen bonds : bond 0.03969 ( 372) hydrogen bonds : angle 4.38698 ( 1053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: R 277 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6961 (t80) REVERT: A 255 ASN cc_start: 0.8390 (m-40) cc_final: 0.8180 (m110) REVERT: A 309 ASP cc_start: 0.7854 (t0) cc_final: 0.7585 (t0) REVERT: A 318 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6228 (tm-30) REVERT: S 93 MET cc_start: 0.7978 (ttt) cc_final: 0.7751 (ttt) REVERT: S 202 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7344 (mtm-85) REVERT: S 235 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.6130 (t80) REVERT: B 234 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8642 (t80) outliers start: 44 outliers final: 35 residues processed: 156 average time/residue: 0.0956 time to fit residues: 20.7762 Evaluate side-chains 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.0370 chunk 86 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.160306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111358 restraints weight = 11042.234| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.07 r_work: 0.3190 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8706 Z= 0.100 Angle : 0.483 10.519 11843 Z= 0.253 Chirality : 0.041 0.140 1358 Planarity : 0.004 0.051 1499 Dihedral : 4.353 38.258 1221 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.02 % Allowed : 26.18 % Favored : 69.80 % 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 aren not related in a simple way. whole: 0.05 (0.25), residues: 1106 helix: 1.51 (0.28), residues: 369 sheet: -0.00 (0.31), residues: 263 loop : -1.12 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 160 TYR 0.018 0.001 TYR S 235 PHE 0.019 0.001 PHE R 276 TRP 0.021 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8703) covalent geometry : angle 0.48323 (11837) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.82530 ( 6) hydrogen bonds : bond 0.03299 ( 372) hydrogen bonds : angle 4.17995 ( 1053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: R 45 ASN cc_start: 0.7813 (m-40) cc_final: 0.7393 (m110) REVERT: R 277 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6974 (t80) REVERT: A 309 ASP cc_start: 0.7886 (t0) cc_final: 0.7606 (t0) REVERT: A 318 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6227 (tm-30) REVERT: S 93 MET cc_start: 0.7930 (ttt) cc_final: 0.7665 (ttt) REVERT: S 202 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7247 (mtm-85) REVERT: S 235 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.5687 (t80) REVERT: B 234 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8593 (t80) outliers start: 35 outliers final: 26 residues processed: 153 average time/residue: 0.0876 time to fit residues: 18.7724 Evaluate side-chains 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 80 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 68 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109880 restraints weight = 10908.871| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.92 r_work: 0.3230 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8706 Z= 0.089 Angle : 0.471 10.556 11843 Z= 0.247 Chirality : 0.041 0.141 1358 Planarity : 0.004 0.054 1499 Dihedral : 4.187 34.555 1221 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.76 % Allowed : 27.90 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.25), residues: 1106 helix: 1.53 (0.28), residues: 372 sheet: 0.23 (0.32), residues: 247 loop : -1.08 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 160 TYR 0.015 0.001 TYR S 235 PHE 0.019 0.001 PHE R 276 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 8703) covalent geometry : angle 0.47099 (11837) SS BOND : bond 0.00481 ( 3) SS BOND : angle 0.76258 ( 6) hydrogen bonds : bond 0.03024 ( 372) hydrogen bonds : angle 4.06959 ( 1053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.256 Fit side-chains REVERT: R 45 ASN cc_start: 0.7801 (m-40) cc_final: 0.7597 (m110) REVERT: R 277 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.7080 (t80) REVERT: A 309 ASP cc_start: 0.7894 (t0) cc_final: 0.7593 (t0) REVERT: A 318 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: S 93 MET cc_start: 0.7928 (ttt) cc_final: 0.7638 (ttt) REVERT: S 160 ARG cc_start: 0.7329 (mtp-110) cc_final: 0.7122 (mtp-110) REVERT: S 202 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7274 (ptp90) REVERT: S 235 TYR cc_start: 0.6184 (OUTLIER) cc_final: 0.5664 (t80) outliers start: 24 outliers final: 18 residues processed: 142 average time/residue: 0.0850 time to fit residues: 16.7023 Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.161017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108070 restraints weight = 10994.849| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.88 r_work: 0.3216 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8706 Z= 0.102 Angle : 0.480 10.248 11843 Z= 0.251 Chirality : 0.041 0.131 1358 Planarity : 0.004 0.054 1499 Dihedral : 4.178 33.950 1221 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.87 % Allowed : 27.90 % Favored : 69.23 % 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 aren not related in a simple way. whole: 0.20 (0.25), residues: 1106 helix: 1.62 (0.28), residues: 371 sheet: 0.26 (0.32), residues: 246 loop : -1.11 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 160 TYR 0.016 0.001 TYR S 235 PHE 0.023 0.001 PHE R 276 TRP 0.028 0.001 TRP R 188 HIS 0.004 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8703) covalent geometry : angle 0.47942 (11837) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.92327 ( 6) hydrogen bonds : bond 0.03153 ( 372) hydrogen bonds : angle 4.03334 ( 1053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: R 45 ASN cc_start: 0.7830 (m-40) cc_final: 0.7620 (m110) REVERT: R 259 HIS cc_start: 0.7856 (t70) cc_final: 0.7610 (t70) REVERT: R 277 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.7111 (t80) REVERT: A 309 ASP cc_start: 0.7927 (t0) cc_final: 0.7648 (t0) REVERT: A 318 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6254 (tm-30) REVERT: S 93 MET cc_start: 0.7942 (ttt) cc_final: 0.7658 (ttt) REVERT: S 202 ARG cc_start: 0.7512 (mtm-85) cc_final: 0.7295 (ptp90) outliers start: 25 outliers final: 21 residues processed: 139 average time/residue: 0.0941 time to fit residues: 18.0779 Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 119 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.161974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109768 restraints weight = 10884.306| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.79 r_work: 0.3233 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8706 Z= 0.092 Angle : 0.469 9.672 11843 Z= 0.246 Chirality : 0.040 0.132 1358 Planarity : 0.004 0.048 1499 Dihedral : 4.077 31.599 1221 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.99 % Allowed : 27.55 % Favored : 69.46 % 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 aren not related in a simple way. whole: 0.19 (0.25), residues: 1106 helix: 1.69 (0.28), residues: 371 sheet: 0.12 (0.31), residues: 258 loop : -1.12 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 160 TYR 0.019 0.001 TYR S 235 PHE 0.023 0.001 PHE R 276 TRP 0.024 0.001 TRP R 188 HIS 0.004 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8703) covalent geometry : angle 0.46874 (11837) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.89456 ( 6) hydrogen bonds : bond 0.03031 ( 372) hydrogen bonds : angle 3.96533 ( 1053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.99 seconds wall clock time: 38 minutes 40.32 seconds (2320.32 seconds total)