Starting phenix.real_space_refine on Wed Jan 14 00:14:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rkf_24496/01_2026/7rkf_24496.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rkf_24496/01_2026/7rkf_24496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rkf_24496/01_2026/7rkf_24496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rkf_24496/01_2026/7rkf_24496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rkf_24496/01_2026/7rkf_24496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rkf_24496/01_2026/7rkf_24496.map" } resolution = 4.0 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 6742 2.51 5 N 1797 2.21 5 O 1952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10563 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2880 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 341} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2559 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1753 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 529 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PCA:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2419 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 285} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.60, per 1000 atoms: 0.25 Number of scatterers: 10563 At special positions: 0 Unit cell: (100.3, 138.55, 148.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 2 15.00 O 1952 8.00 N 1797 7.00 C 6742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.03 Simple disulfide: pdb=" SG CYS L 12 " - pdb=" SG CYS L 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " 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 Links applied NAG-ASN " NAG L 101 " - " ASN L 9 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 566.1 milliseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 41.6% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 4.136A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.643A pdb=" N PHE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 69 through 91 Processing helix chain 'A' and resid 97 through 103 removed outlier: 3.589A pdb=" N LYS A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.068A pdb=" N GLU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 131 removed outlier: 3.569A pdb=" N VAL A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 157 through 163 removed outlier: 3.551A pdb=" N ILE A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.970A pdb=" N LEU A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.615A pdb=" N HIS A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.153A pdb=" N ASP A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.530A pdb=" N ILE A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.504A pdb=" N LEU A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.932A pdb=" N TYR A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.981A pdb=" N TYR A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.583A pdb=" N ALA A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 3.749A pdb=" N ALA A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.794A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.489A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.585A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.567A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.522A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.586A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.162A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 22 No H-bonds generated for 'chain 'L' and resid 20 through 22' Processing helix chain 'L' and resid 55 through 67 removed outlier: 4.125A pdb=" N LYS L 59 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 58 Proline residue: R 34 - end of helix removed outlier: 3.749A pdb=" N PHE R 52 " --> pdb=" O SER R 48 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 removed outlier: 3.599A pdb=" N VAL R 70 " --> pdb=" O CYS R 66 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.766A pdb=" N TRP R 89 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU R 94 " --> pdb=" O MET R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 102 Processing helix chain 'R' and resid 103 through 136 removed outlier: 4.089A pdb=" N LEU R 107 " --> pdb=" O PRO R 103 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA R 126 " --> pdb=" O ILE R 122 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL R 134 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 159 removed outlier: 3.683A pdb=" N ALA R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 163 Processing helix chain 'R' and resid 168 through 172 removed outlier: 3.864A pdb=" N ASN R 171 " --> pdb=" O LYS R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 197 Processing helix chain 'R' and resid 197 through 218 removed outlier: 3.737A pdb=" N ARG R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE R 214 " --> pdb=" O ARG R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 256 removed outlier: 3.850A pdb=" N ILE R 226 " --> pdb=" O HIS R 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP R 241 " --> pdb=" O PHE R 237 " (cutoff:3.500A) Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 262 through 281 removed outlier: 3.669A pdb=" N PHE R 281 " --> pdb=" O GLU R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 285 removed outlier: 3.511A pdb=" N CYS R 285 " --> pdb=" O CYS R 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 282 through 285' Processing helix chain 'R' and resid 286 through 292 Processing helix chain 'R' and resid 295 through 310 removed outlier: 3.949A pdb=" N GLU R 308 " --> pdb=" O CYS R 304 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.560A pdb=" N MET A 197 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 34 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 196 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 38 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N SER A 219 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS A 35 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N MET A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 37 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 223 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 39 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ALA A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A 220 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE A 266 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 222 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASN A 268 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 224 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 319 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS A 321 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.982A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.606A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.208A 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: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.176A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.009A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.778A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.089A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.149A pdb=" N VAL D 12 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR D 50 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D 59 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 134 through 136 removed outlier: 5.974A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 143 through 147 Processing sheet with id=AB4, first strand: chain 'D' and resid 174 through 178 removed outlier: 5.640A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 218 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 24 through 27 420 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3406 1.35 - 1.47: 2689 1.47 - 1.59: 4596 1.59 - 1.71: 3 1.71 - 1.83: 100 Bond restraints: 10794 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.462 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C1 NAG L 101 " pdb=" O5 NAG L 101 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.53e+00 bond pdb=" C5 GDP A 401 " pdb=" C4 GDP A 401 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" CB MET A 53 " pdb=" CG MET A 53 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CB GLN B 75 " pdb=" CG GLN B 75 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.63e+00 ... (remaining 10789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 14338 2.20 - 4.41: 271 4.41 - 6.61: 29 6.61 - 8.82: 6 8.82 - 11.02: 5 Bond angle restraints: 14649 Sorted by residual: angle pdb=" CA PCA L 1 " pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 114.17 103.15 11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.60 116.81 5.79 1.88e+00 2.83e-01 9.47e+00 angle pdb=" CB MET R 164 " pdb=" CG MET R 164 " pdb=" SD MET R 164 " ideal model delta sigma weight residual 112.70 121.53 -8.83 3.00e+00 1.11e-01 8.67e+00 angle pdb=" C ALA B 92 " pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 123.33 120.81 2.52 8.70e-01 1.32e+00 8.42e+00 angle pdb=" CA MET R 164 " pdb=" CB MET R 164 " pdb=" CG MET R 164 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 ... (remaining 14644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.26: 6200 29.26 - 58.53: 210 58.53 - 87.79: 18 87.79 - 117.06: 1 117.06 - 146.32: 2 Dihedral angle restraints: 6431 sinusoidal: 2522 harmonic: 3909 Sorted by residual: dihedral pdb=" O2B GDP A 401 " pdb=" O3A GDP A 401 " pdb=" PB GDP A 401 " pdb=" PA GDP A 401 " ideal model delta sinusoidal sigma weight residual -180.00 -33.68 -146.32 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" C5' GDP A 401 " pdb=" O5' GDP A 401 " pdb=" PA GDP A 401 " pdb=" O3A GDP A 401 " ideal model delta sinusoidal sigma weight residual 179.98 38.72 141.26 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" CA ARG D 179 " pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 6428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1077 0.038 - 0.076: 407 0.076 - 0.114: 150 0.114 - 0.153: 26 0.153 - 0.191: 7 Chirality restraints: 1667 Sorted by residual: chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" C1 NAG L 101 " pdb=" ND2 ASN L 9 " pdb=" C2 NAG L 101 " pdb=" O5 NAG L 101 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ASP D 74 " pdb=" N ASP D 74 " pdb=" C ASP D 74 " pdb=" CB ASP D 74 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 1664 not shown) Planarity restraints: 1847 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 311 " -0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO A 312 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 235 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C LEU R 235 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU R 235 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL R 236 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO C 55 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.023 5.00e-02 4.00e+02 ... (remaining 1844 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1805 2.77 - 3.30: 10076 3.30 - 3.83: 15665 3.83 - 4.37: 16789 4.37 - 4.90: 29571 Nonbonded interactions: 73906 Sorted by model distance: nonbonded pdb=" ND2 ASN R 51 " pdb=" OD2 ASP R 79 " model vdw 2.232 3.120 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.251 3.120 nonbonded pdb=" ND2 ASN R 74 " pdb=" OG SER R 148 " model vdw 2.260 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.283 3.040 nonbonded pdb=" ND2 ASN B 119 " pdb=" O GLY B 144 " model vdw 2.286 3.120 ... (remaining 73901 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 group one per residue 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: 2.520 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.700 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 10801 Z= 0.215 Angle : 0.765 11.020 14664 Z= 0.406 Chirality : 0.046 0.191 1667 Planarity : 0.005 0.099 1846 Dihedral : 14.450 146.320 3889 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.22), residues: 1319 helix: 0.72 (0.24), residues: 443 sheet: -1.09 (0.30), residues: 273 loop : -1.53 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 206 TYR 0.019 0.002 TYR A 74 PHE 0.025 0.002 PHE B 234 TRP 0.015 0.002 TRP A 210 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00491 (10794) covalent geometry : angle 0.76337 (14649) SS BOND : bond 0.00570 ( 6) SS BOND : angle 1.34452 ( 12) hydrogen bonds : bond 0.16003 ( 420) hydrogen bonds : angle 5.83139 ( 1194) link_NAG-ASN : bond 0.00504 ( 1) link_NAG-ASN : angle 2.76129 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7428 (tpt) cc_final: 0.7142 (tpp) REVERT: B 188 MET cc_start: 0.8659 (mmm) cc_final: 0.8301 (mmt) REVERT: D 82 GLN cc_start: 0.7141 (mm110) cc_final: 0.6712 (mt0) REVERT: D 93 MET cc_start: 0.6893 (tpt) cc_final: 0.6203 (tpt) REVERT: L 14 LYS cc_start: 0.7298 (tptt) cc_final: 0.6445 (mptt) REVERT: R 178 ASP cc_start: 0.6970 (t0) cc_final: 0.6763 (t70) REVERT: R 257 LYS cc_start: 0.8785 (mtpt) cc_final: 0.7729 (pttp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1075 time to fit residues: 29.3489 Evaluate side-chains 161 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 75 GLN A 76 ASN A 103 ASN A 203 GLN A 216 ASN A 231 GLN A 330 ASN B 17 GLN B 54 HIS B 266 HIS B 340 ASN C 18 GLN D 35 HIS D 220 HIS L 64 HIS ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121083 restraints weight = 16798.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120521 restraints weight = 23017.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121516 restraints weight = 21885.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123915 restraints weight = 14358.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124058 restraints weight = 10305.763| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10801 Z= 0.129 Angle : 0.609 6.676 14664 Z= 0.320 Chirality : 0.042 0.214 1667 Planarity : 0.004 0.056 1846 Dihedral : 6.878 146.039 1498 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.41 % Allowed : 10.76 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1319 helix: 1.35 (0.24), residues: 457 sheet: -0.71 (0.31), residues: 274 loop : -1.38 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 221 TYR 0.029 0.001 TYR A 350 PHE 0.029 0.001 PHE R 111 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00264 (10794) covalent geometry : angle 0.60781 (14649) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.97661 ( 12) hydrogen bonds : bond 0.05164 ( 420) hydrogen bonds : angle 4.62830 ( 1194) link_NAG-ASN : bond 0.00530 ( 1) link_NAG-ASN : angle 1.82186 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8559 (t0) REVERT: A 88 MET cc_start: 0.7348 (tpt) cc_final: 0.7079 (tpp) REVERT: D 82 GLN cc_start: 0.6966 (mm110) cc_final: 0.6641 (mt0) REVERT: L 14 LYS cc_start: 0.7286 (tptt) cc_final: 0.6470 (mptt) REVERT: R 142 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6699 (mmtt) REVERT: R 257 LYS cc_start: 0.8765 (mtpt) cc_final: 0.7802 (pttp) outliers start: 16 outliers final: 5 residues processed: 190 average time/residue: 0.1082 time to fit residues: 28.9201 Evaluate side-chains 170 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 295 ASN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.147665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119740 restraints weight = 17138.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118250 restraints weight = 22343.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119749 restraints weight = 22921.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120459 restraints weight = 13599.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121192 restraints weight = 11545.569| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10801 Z= 0.129 Angle : 0.588 8.494 14664 Z= 0.307 Chirality : 0.042 0.202 1667 Planarity : 0.004 0.043 1846 Dihedral : 6.566 142.482 1498 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.76 % Allowed : 14.90 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1319 helix: 1.54 (0.24), residues: 452 sheet: -0.46 (0.32), residues: 274 loop : -1.31 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 206 TYR 0.016 0.001 TYR A 74 PHE 0.020 0.001 PHE R 111 TRP 0.012 0.001 TRP D 164 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00277 (10794) covalent geometry : angle 0.58700 (14649) SS BOND : bond 0.00332 ( 6) SS BOND : angle 0.95131 ( 12) hydrogen bonds : bond 0.04859 ( 420) hydrogen bonds : angle 4.39975 ( 1194) link_NAG-ASN : bond 0.00324 ( 1) link_NAG-ASN : angle 1.68249 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7239 (tm-30) REVERT: D 82 GLN cc_start: 0.7040 (mm110) cc_final: 0.6763 (mt0) REVERT: L 14 LYS cc_start: 0.7356 (tptt) cc_final: 0.6720 (tptp) REVERT: R 257 LYS cc_start: 0.8847 (mtpt) cc_final: 0.7775 (pttp) outliers start: 20 outliers final: 9 residues processed: 187 average time/residue: 0.1028 time to fit residues: 27.1037 Evaluate side-chains 171 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 46 PHE Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 53 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 0.0060 chunk 10 optimal weight: 0.4980 chunk 85 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 346 ASN L 29 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123344 restraints weight = 17291.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122225 restraints weight = 21480.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123191 restraints weight = 20810.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125295 restraints weight = 14124.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125480 restraints weight = 10795.637| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10801 Z= 0.104 Angle : 0.559 11.220 14664 Z= 0.285 Chirality : 0.041 0.212 1667 Planarity : 0.003 0.038 1846 Dihedral : 6.154 138.180 1498 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.12 % Allowed : 15.43 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1319 helix: 1.62 (0.24), residues: 464 sheet: -0.18 (0.32), residues: 268 loop : -1.28 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 206 TYR 0.014 0.001 TYR A 74 PHE 0.021 0.001 PHE R 111 TRP 0.012 0.001 TRP D 47 HIS 0.003 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00204 (10794) covalent geometry : angle 0.55904 (14649) SS BOND : bond 0.00248 ( 6) SS BOND : angle 0.72941 ( 12) hydrogen bonds : bond 0.03800 ( 420) hydrogen bonds : angle 4.10493 ( 1194) link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 1.38788 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6508 (tpt) REVERT: A 48 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8230 (m) REVERT: A 88 MET cc_start: 0.7195 (tpp) cc_final: 0.6963 (tpp) REVERT: B 95 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8218 (pp) REVERT: D 86 LEU cc_start: 0.7235 (pt) cc_final: 0.6944 (pp) REVERT: D 91 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8241 (t) REVERT: D 113 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7388 (tm-30) REVERT: L 14 LYS cc_start: 0.7286 (tptt) cc_final: 0.6634 (tptp) REVERT: L 60 ASP cc_start: 0.7529 (m-30) cc_final: 0.7036 (m-30) REVERT: R 142 LYS cc_start: 0.6970 (mmmt) cc_final: 0.6512 (mmtt) REVERT: R 257 LYS cc_start: 0.8845 (mtpt) cc_final: 0.7730 (pttp) outliers start: 24 outliers final: 9 residues processed: 208 average time/residue: 0.0959 time to fit residues: 28.2166 Evaluate side-chains 182 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 46 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 346 ASN A 351 ASN B 88 ASN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.144364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115469 restraints weight = 17401.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114614 restraints weight = 23185.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115614 restraints weight = 21592.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117816 restraints weight = 13990.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118133 restraints weight = 9739.315| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10801 Z= 0.178 Angle : 0.653 9.678 14664 Z= 0.337 Chirality : 0.044 0.202 1667 Planarity : 0.004 0.037 1846 Dihedral : 6.148 127.957 1498 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.03 % Allowed : 17.99 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.23), residues: 1319 helix: 1.43 (0.24), residues: 461 sheet: -0.33 (0.32), residues: 276 loop : -1.37 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 206 TYR 0.013 0.001 TYR R 206 PHE 0.020 0.002 PHE B 199 TRP 0.013 0.001 TRP B 297 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00412 (10794) covalent geometry : angle 0.65206 (14649) SS BOND : bond 0.00550 ( 6) SS BOND : angle 0.98257 ( 12) hydrogen bonds : bond 0.05509 ( 420) hydrogen bonds : angle 4.38099 ( 1194) link_NAG-ASN : bond 0.00384 ( 1) link_NAG-ASN : angle 1.24015 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7379 (tm-30) REVERT: A 88 MET cc_start: 0.7426 (tpp) cc_final: 0.7209 (tpp) REVERT: B 95 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8401 (pp) REVERT: B 120 ILE cc_start: 0.8843 (mm) cc_final: 0.8614 (mm) REVERT: B 188 MET cc_start: 0.8908 (mmt) cc_final: 0.8687 (mmm) REVERT: D 82 GLN cc_start: 0.7179 (mm110) cc_final: 0.6938 (mt0) REVERT: D 86 LEU cc_start: 0.7421 (pt) cc_final: 0.7155 (pp) REVERT: D 93 MET cc_start: 0.7047 (tpt) cc_final: 0.6630 (tpt) REVERT: L 14 LYS cc_start: 0.7256 (tptt) cc_final: 0.6587 (tptp) REVERT: R 124 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8085 (tm-30) REVERT: R 257 LYS cc_start: 0.8950 (mtpt) cc_final: 0.7820 (pttp) REVERT: R 276 THR cc_start: 0.9314 (t) cc_final: 0.9082 (t) outliers start: 23 outliers final: 14 residues processed: 194 average time/residue: 0.1030 time to fit residues: 28.2528 Evaluate side-chains 184 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 184 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 92 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114739 restraints weight = 17440.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116014 restraints weight = 25506.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117128 restraints weight = 21442.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117483 restraints weight = 13475.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118420 restraints weight = 12061.319| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10801 Z= 0.170 Angle : 0.642 10.073 14664 Z= 0.331 Chirality : 0.044 0.238 1667 Planarity : 0.004 0.034 1846 Dihedral : 6.051 121.691 1498 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.38 % Allowed : 18.61 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.23), residues: 1319 helix: 1.47 (0.24), residues: 454 sheet: -0.46 (0.31), residues: 279 loop : -1.32 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 206 TYR 0.011 0.001 TYR D 102 PHE 0.020 0.002 PHE D 200 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS R 162 Details of bonding type rmsd covalent geometry : bond 0.00394 (10794) covalent geometry : angle 0.64164 (14649) SS BOND : bond 0.00630 ( 6) SS BOND : angle 0.88597 ( 12) hydrogen bonds : bond 0.05289 ( 420) hydrogen bonds : angle 4.34143 ( 1194) link_NAG-ASN : bond 0.00344 ( 1) link_NAG-ASN : angle 1.72958 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7299 (tpp) cc_final: 0.7090 (tpp) REVERT: B 95 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8404 (pp) REVERT: B 120 ILE cc_start: 0.8838 (mm) cc_final: 0.8618 (mm) REVERT: B 188 MET cc_start: 0.8916 (mmt) cc_final: 0.8676 (mmm) REVERT: D 82 GLN cc_start: 0.7112 (mm110) cc_final: 0.6896 (mt0) REVERT: L 14 LYS cc_start: 0.7276 (tptt) cc_final: 0.6641 (tptp) REVERT: R 124 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8147 (tm-30) REVERT: R 142 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7042 (mmmt) REVERT: R 257 LYS cc_start: 0.8978 (mtpt) cc_final: 0.7901 (pttp) REVERT: R 276 THR cc_start: 0.9337 (t) cc_final: 0.9123 (t) outliers start: 27 outliers final: 17 residues processed: 194 average time/residue: 0.1006 time to fit residues: 27.8158 Evaluate side-chains 184 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 184 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 103 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 25 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122451 restraints weight = 16916.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122996 restraints weight = 29535.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124196 restraints weight = 24719.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124655 restraints weight = 14826.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125340 restraints weight = 13049.708| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10801 Z= 0.122 Angle : 0.598 8.896 14664 Z= 0.307 Chirality : 0.042 0.209 1667 Planarity : 0.003 0.034 1846 Dihedral : 5.740 114.301 1498 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.20 % Allowed : 19.05 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1319 helix: 1.54 (0.24), residues: 461 sheet: -0.20 (0.32), residues: 270 loop : -1.28 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 206 TYR 0.015 0.001 TYR A 350 PHE 0.023 0.001 PHE D 200 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS R 162 Details of bonding type rmsd covalent geometry : bond 0.00267 (10794) covalent geometry : angle 0.59775 (14649) SS BOND : bond 0.00562 ( 6) SS BOND : angle 0.90483 ( 12) hydrogen bonds : bond 0.04431 ( 420) hydrogen bonds : angle 4.19679 ( 1194) link_NAG-ASN : bond 0.00314 ( 1) link_NAG-ASN : angle 1.48534 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7288 (tm-30) REVERT: B 95 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8504 (pp) REVERT: L 14 LYS cc_start: 0.7206 (tptt) cc_final: 0.6653 (tptp) REVERT: R 142 LYS cc_start: 0.7506 (mmmt) cc_final: 0.6911 (mmtt) REVERT: R 257 LYS cc_start: 0.8876 (mtpt) cc_final: 0.7736 (pttp) REVERT: R 276 THR cc_start: 0.9304 (t) cc_final: 0.9095 (t) outliers start: 25 outliers final: 16 residues processed: 189 average time/residue: 0.1023 time to fit residues: 27.4825 Evaluate side-chains 185 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 46 PHE Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 184 TYR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 71 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 GLN R 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112871 restraints weight = 17598.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114507 restraints weight = 27916.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115156 restraints weight = 20279.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117359 restraints weight = 14192.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117405 restraints weight = 10268.792| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10801 Z= 0.229 Angle : 0.713 10.986 14664 Z= 0.369 Chirality : 0.045 0.193 1667 Planarity : 0.004 0.039 1846 Dihedral : 5.862 109.610 1498 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.20 % Allowed : 19.58 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.23), residues: 1319 helix: 1.34 (0.24), residues: 449 sheet: -0.50 (0.31), residues: 275 loop : -1.38 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 206 TYR 0.015 0.002 TYR R 206 PHE 0.032 0.002 PHE A 188 TRP 0.010 0.001 TRP B 297 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00545 (10794) covalent geometry : angle 0.71275 (14649) SS BOND : bond 0.00599 ( 6) SS BOND : angle 1.09510 ( 12) hydrogen bonds : bond 0.06117 ( 420) hydrogen bonds : angle 4.56606 ( 1194) link_NAG-ASN : bond 0.00417 ( 1) link_NAG-ASN : angle 1.44261 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7398 (tm-30) REVERT: B 95 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8438 (pp) REVERT: R 18 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.6054 (pm20) REVERT: R 124 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8147 (tm-30) REVERT: R 142 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7247 (mmtt) REVERT: R 257 LYS cc_start: 0.9025 (mtpt) cc_final: 0.7944 (pttp) outliers start: 25 outliers final: 17 residues processed: 190 average time/residue: 0.1032 time to fit residues: 27.6759 Evaluate side-chains 182 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 184 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN R 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114832 restraints weight = 17495.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114873 restraints weight = 22212.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116150 restraints weight = 20676.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116924 restraints weight = 11876.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117634 restraints weight = 10376.419| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10801 Z= 0.142 Angle : 0.653 10.410 14664 Z= 0.334 Chirality : 0.043 0.209 1667 Planarity : 0.004 0.035 1846 Dihedral : 5.478 102.471 1498 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.85 % Allowed : 20.72 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.23), residues: 1319 helix: 1.47 (0.25), residues: 455 sheet: -0.33 (0.31), residues: 269 loop : -1.41 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 206 TYR 0.014 0.001 TYR A 350 PHE 0.030 0.002 PHE R 121 TRP 0.012 0.001 TRP D 47 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00321 (10794) covalent geometry : angle 0.65250 (14649) SS BOND : bond 0.00677 ( 6) SS BOND : angle 1.08299 ( 12) hydrogen bonds : bond 0.04971 ( 420) hydrogen bonds : angle 4.34032 ( 1194) link_NAG-ASN : bond 0.00434 ( 1) link_NAG-ASN : angle 1.45743 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 197 MET cc_start: 0.8398 (ptp) cc_final: 0.8127 (ptp) REVERT: B 95 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8412 (pp) REVERT: L 14 LYS cc_start: 0.7086 (tptm) cc_final: 0.6626 (tptp) REVERT: L 36 LYS cc_start: 0.6366 (mmmt) cc_final: 0.6006 (mmtt) REVERT: R 257 LYS cc_start: 0.9015 (mtpt) cc_final: 0.7939 (pttp) outliers start: 21 outliers final: 17 residues processed: 181 average time/residue: 0.0953 time to fit residues: 24.4375 Evaluate side-chains 181 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 46 PHE Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 184 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN A 260 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN R 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115375 restraints weight = 17510.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116166 restraints weight = 21837.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117041 restraints weight = 21713.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117742 restraints weight = 12519.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118372 restraints weight = 10566.919| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 10801 Z= 0.173 Angle : 0.915 59.199 14664 Z= 0.515 Chirality : 0.043 0.358 1667 Planarity : 0.004 0.045 1846 Dihedral : 5.472 102.402 1498 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.76 % Allowed : 20.81 % Favored : 77.43 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1319 helix: 1.47 (0.25), residues: 455 sheet: -0.32 (0.31), residues: 269 loop : -1.41 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 206 TYR 0.014 0.001 TYR A 350 PHE 0.028 0.002 PHE D 200 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00360 (10794) covalent geometry : angle 0.91037 (14649) SS BOND : bond 0.00591 ( 6) SS BOND : angle 3.18009 ( 12) hydrogen bonds : bond 0.04947 ( 420) hydrogen bonds : angle 4.34897 ( 1194) link_NAG-ASN : bond 0.00386 ( 1) link_NAG-ASN : angle 1.46747 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 197 MET cc_start: 0.8378 (ptp) cc_final: 0.8125 (ptp) REVERT: B 95 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8370 (pp) REVERT: L 14 LYS cc_start: 0.7081 (tptm) cc_final: 0.6618 (tptp) REVERT: L 36 LYS cc_start: 0.6361 (mmmt) cc_final: 0.6046 (mmtt) REVERT: R 257 LYS cc_start: 0.9020 (mtpt) cc_final: 0.7930 (pttp) outliers start: 20 outliers final: 17 residues processed: 176 average time/residue: 0.0997 time to fit residues: 24.8923 Evaluate side-chains 178 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain R residue 46 PHE Chi-restraints excluded: chain R residue 184 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 chunk 118 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115558 restraints weight = 17738.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115107 restraints weight = 26918.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116152 restraints weight = 22539.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118713 restraints weight = 15090.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119003 restraints weight = 10301.376| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 10801 Z= 0.173 Angle : 0.915 59.199 14664 Z= 0.515 Chirality : 0.043 0.358 1667 Planarity : 0.004 0.045 1846 Dihedral : 5.472 102.402 1498 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.59 % Allowed : 20.81 % Favored : 77.60 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1319 helix: 1.47 (0.25), residues: 455 sheet: -0.32 (0.31), residues: 269 loop : -1.41 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 206 TYR 0.014 0.001 TYR A 350 PHE 0.028 0.002 PHE D 200 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00360 (10794) covalent geometry : angle 0.91037 (14649) SS BOND : bond 0.00591 ( 6) SS BOND : angle 3.18009 ( 12) hydrogen bonds : bond 0.04947 ( 420) hydrogen bonds : angle 4.34897 ( 1194) link_NAG-ASN : bond 0.00386 ( 1) link_NAG-ASN : angle 1.46747 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.40 seconds wall clock time: 29 minutes 10.75 seconds (1750.75 seconds total)