Starting phenix.real_space_refine on Thu May 1 07:29:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dne_27564/05_2025/8dne_27564.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dne_27564/05_2025/8dne_27564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dne_27564/05_2025/8dne_27564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dne_27564/05_2025/8dne_27564.map" model { file = "/net/cci-nas-00/data/ceres_data/8dne_27564/05_2025/8dne_27564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dne_27564/05_2025/8dne_27564.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.065 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 6841 2.51 5 N 1609 2.21 5 O 1795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10281 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2976 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 2 Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2979 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain breaks: 2 Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.10, per 1000 atoms: 0.59 Number of scatterers: 10281 At special positions: 0 Unit cell: (91.8, 85.32, 136.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1795 8.00 N 1609 7.00 C 6841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 52.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.603A pdb=" N ILE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.557A pdb=" N ILE A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.702A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 191 removed outlier: 3.597A pdb=" N GLY A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.581A pdb=" N VAL A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 240 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 21 through 47 removed outlier: 3.959A pdb=" N ILE B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 4.431A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 82 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.658A pdb=" N GLU B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 88' Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.733A pdb=" N THR B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 126 removed outlier: 3.732A pdb=" N VAL B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 138 removed outlier: 5.123A pdb=" N TYR B 138 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 3.872A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 180 removed outlier: 3.948A pdb=" N GLY B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.511A pdb=" N LEU B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 223 through 256 Proline residue: B 235 - end of helix removed outlier: 3.579A pdb=" N LEU B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 27 removed outlier: 4.105A pdb=" N LEU C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 129 removed outlier: 4.974A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 4.229A pdb=" N ASN C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.527A pdb=" N TYR C 142 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 173 through 190 removed outlier: 3.528A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 208 removed outlier: 4.010A pdb=" N VAL C 204 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 26 through 44 Proline residue: D 32 - end of helix Processing helix chain 'D' and resid 55 through 82 Proline residue: D 70 - end of helix removed outlier: 3.613A pdb=" N THR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.616A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 100 through 129 removed outlier: 3.628A pdb=" N VAL D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 138 removed outlier: 4.900A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 165 removed outlier: 3.963A pdb=" N SER D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR D 160 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.962A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 217 removed outlier: 4.362A pdb=" N VAL D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 233 through 256 removed outlier: 3.520A pdb=" N LEU D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 43 removed outlier: 7.110A pdb=" N LEU A 34 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LYS A 12 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 36 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LYS A 10 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS A 38 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TRP A 8 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE A 40 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 removed outlier: 6.588A pdb=" N VAL A 85 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP A 166 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A 87 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 51 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU A 214 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 53 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 211 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A 222 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 213 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 265 removed outlier: 5.200A pdb=" N ILE A 259 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU A 287 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN C 390 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C 388 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 276 removed outlier: 5.999A pdb=" N PHE A 274 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 373 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS A 350 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 296 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 310 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP A 303 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 394 removed outlier: 3.549A pdb=" N LYS C 333 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 331 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 392 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 394 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS C 327 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 44 removed outlier: 3.569A pdb=" N GLU C 32 " --> pdb=" O TYR C 13 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS C 9 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS C 38 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL C 7 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE C 40 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE C 5 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 42 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ARG C 3 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C 7 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS C 75 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 84 through 87 removed outlier: 4.346A pdb=" N ASP C 166 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE C 163 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL C 197 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 165 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 49 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU C 214 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 53 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 276 removed outlier: 6.619A pdb=" N PHE C 274 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLY C 373 " --> pdb=" O PHE C 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 313 removed outlier: 6.714A pdb=" N ILE C 301 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY C 311 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 299 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN C 313 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 297 " --> pdb=" O ASN C 313 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1443 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: 3.09 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3019 1.34 - 1.46: 1762 1.46 - 1.57: 5707 1.57 - 1.69: 10 1.69 - 1.81: 46 Bond restraints: 10544 Sorted by residual: bond pdb=" N ILE C 135 " pdb=" CA ILE C 135 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.28e+00 bond pdb=" N VAL D 186 " pdb=" CA VAL D 186 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.41e-02 5.03e+03 6.38e+00 bond pdb=" N VAL B 186 " pdb=" CA VAL B 186 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.51e+00 bond pdb=" N TYR D 187 " pdb=" CA TYR D 187 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.21e-02 6.83e+03 5.30e+00 bond pdb=" O5' ATP C 502 " pdb=" PA ATP C 502 " ideal model delta sigma weight residual 1.579 1.602 -0.023 1.10e-02 8.26e+03 4.52e+00 ... (remaining 10539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 13977 1.91 - 3.82: 238 3.82 - 5.73: 45 5.73 - 7.64: 3 7.64 - 9.55: 6 Bond angle restraints: 14269 Sorted by residual: angle pdb=" PA ATP A 502 " pdb=" O3A ATP A 502 " pdb=" PB ATP A 502 " ideal model delta sigma weight residual 136.83 127.51 9.32 1.00e+00 1.00e+00 8.69e+01 angle pdb=" PB ATP A 502 " pdb=" O3B ATP A 502 " pdb=" PG ATP A 502 " ideal model delta sigma weight residual 139.87 131.01 8.86 1.00e+00 1.00e+00 7.85e+01 angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 131.87 8.00 1.00e+00 1.00e+00 6.39e+01 angle pdb=" N ILE D 47 " pdb=" CA ILE D 47 " pdb=" C ILE D 47 " ideal model delta sigma weight residual 113.71 109.05 4.66 9.50e-01 1.11e+00 2.40e+01 angle pdb=" C5' ATP A 502 " pdb=" O5' ATP A 502 " pdb=" PA ATP A 502 " ideal model delta sigma weight residual 121.27 116.98 4.29 1.00e+00 1.00e+00 1.84e+01 ... (remaining 14264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5533 17.98 - 35.95: 544 35.95 - 53.93: 107 53.93 - 71.90: 12 71.90 - 89.88: 11 Dihedral angle restraints: 6207 sinusoidal: 2568 harmonic: 3639 Sorted by residual: dihedral pdb=" CA ARG A 27 " pdb=" C ARG A 27 " pdb=" N LYS A 28 " pdb=" CA LYS A 28 " ideal model delta harmonic sigma weight residual 180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASN C 95 " pdb=" C ASN C 95 " pdb=" N TYR C 96 " pdb=" CA TYR C 96 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP C 200 " pdb=" C ASP C 200 " pdb=" N MET C 201 " pdb=" CA MET C 201 " ideal model delta harmonic sigma weight residual 180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1461 0.074 - 0.147: 139 0.147 - 0.221: 3 0.221 - 0.294: 0 0.294 - 0.368: 2 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CA VAL D 186 " pdb=" N VAL D 186 " pdb=" C VAL D 186 " pdb=" CB VAL D 186 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA VAL B 186 " pdb=" N VAL B 186 " pdb=" C VAL B 186 " pdb=" CB VAL B 186 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE C 135 " pdb=" CA ILE C 135 " pdb=" CG1 ILE C 135 " pdb=" CG2 ILE C 135 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 1602 not shown) Planarity restraints: 1737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 31 " -0.020 2.00e-02 2.50e+03 1.97e-02 9.71e+00 pdb=" CG TRP D 31 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP D 31 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 31 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 31 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 31 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 31 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 31 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 31 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP D 31 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 193 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO D 194 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 194 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 194 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 31 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 32 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.035 5.00e-02 4.00e+02 ... (remaining 1734 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 28 2.41 - 3.03: 6180 3.03 - 3.65: 15115 3.65 - 4.28: 21782 4.28 - 4.90: 37041 Nonbonded interactions: 80146 Sorted by model distance: nonbonded pdb="MG MG C 501 " pdb=" O1G ATP C 502 " model vdw 1.785 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1G ATP A 502 " model vdw 1.995 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1B ATP A 502 " model vdw 2.020 2.170 nonbonded pdb=" O SER D 119 " pdb=" OG1 THR D 122 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR D 206 " pdb=" O ASP D 221 " model vdw 2.219 3.040 ... (remaining 80141 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 240 or resid 254 through 350 or resid 363 throug \ h 393 or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 350 or resid 363 through 393 or resid 501 throug \ h 502)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.020 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.680 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.004 0.038 10544 Z= 0.174 Angle : 0.654 9.547 14269 Z= 0.382 Chirality : 0.044 0.368 1605 Planarity : 0.004 0.063 1737 Dihedral : 14.834 89.879 3875 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1235 helix: 0.40 (0.22), residues: 574 sheet: 0.67 (0.37), residues: 198 loop : -1.42 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 31 HIS 0.004 0.001 HIS D 45 PHE 0.018 0.001 PHE C 30 TYR 0.021 0.001 TYR B 150 ARG 0.006 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.19205 ( 498) hydrogen bonds : angle 7.55797 ( 1443) covalent geometry : bond 0.00351 (10544) covalent geometry : angle 0.65364 (14269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.764 Fit side-chains REVERT: B 187 TYR cc_start: 0.8141 (p90) cc_final: 0.7819 (p90) REVERT: C 317 MET cc_start: 0.7857 (mtp) cc_final: 0.7651 (mtp) REVERT: C 362 TRP cc_start: 0.7203 (t60) cc_final: 0.6447 (m-90) REVERT: D 87 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6585 (tm-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2064 time to fit residues: 53.6573 Evaluate side-chains 138 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 97 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS B 223 HIS C 56 ASN C 230 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.168952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136041 restraints weight = 15636.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138478 restraints weight = 10264.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141615 restraints weight = 7239.997| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10544 Z= 0.126 Angle : 0.558 7.903 14269 Z= 0.294 Chirality : 0.042 0.170 1605 Planarity : 0.004 0.048 1737 Dihedral : 8.128 85.353 1411 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.45 % Allowed : 10.18 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1235 helix: 1.23 (0.22), residues: 586 sheet: 0.74 (0.37), residues: 199 loop : -1.50 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 31 HIS 0.006 0.001 HIS B 53 PHE 0.022 0.001 PHE D 72 TYR 0.014 0.001 TYR D 150 ARG 0.005 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 498) hydrogen bonds : angle 5.05103 ( 1443) covalent geometry : bond 0.00259 (10544) covalent geometry : angle 0.55768 (14269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5261 (ptt-90) cc_final: 0.4919 (ptp90) REVERT: B 80 ARG cc_start: 0.7869 (ttp-170) cc_final: 0.7457 (ttm170) REVERT: B 110 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 147 MET cc_start: 0.8141 (ttm) cc_final: 0.7914 (ttp) REVERT: B 187 TYR cc_start: 0.8473 (p90) cc_final: 0.8034 (p90) REVERT: B 243 TYR cc_start: 0.7155 (t80) cc_final: 0.6945 (t80) REVERT: C 362 TRP cc_start: 0.7127 (t60) cc_final: 0.6393 (m-90) REVERT: D 8 GLU cc_start: 0.7783 (tp30) cc_final: 0.6873 (tp30) REVERT: D 80 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8228 (ttm170) REVERT: D 87 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6934 (tm-30) REVERT: D 175 PHE cc_start: 0.8412 (t80) cc_final: 0.8038 (t80) outliers start: 5 outliers final: 3 residues processed: 156 average time/residue: 0.2073 time to fit residues: 47.8441 Evaluate side-chains 136 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 183 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117275 restraints weight = 16209.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121279 restraints weight = 9768.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124062 restraints weight = 7074.816| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 10544 Z= 0.383 Angle : 0.800 7.940 14269 Z= 0.416 Chirality : 0.050 0.209 1605 Planarity : 0.005 0.054 1737 Dihedral : 9.550 88.422 1411 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.88 % Allowed : 15.27 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1235 helix: 0.68 (0.21), residues: 586 sheet: 0.32 (0.37), residues: 199 loop : -1.59 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 31 HIS 0.016 0.002 HIS B 53 PHE 0.029 0.003 PHE D 180 TYR 0.035 0.002 TYR B 150 ARG 0.005 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.06907 ( 498) hydrogen bonds : angle 5.28946 ( 1443) covalent geometry : bond 0.00926 (10544) covalent geometry : angle 0.79978 (14269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 165 ILE cc_start: 0.8257 (tt) cc_final: 0.7815 (pt) REVERT: A 263 ARG cc_start: 0.5432 (ptt-90) cc_final: 0.5045 (ptp90) REVERT: A 315 TYR cc_start: 0.5754 (OUTLIER) cc_final: 0.5028 (t80) REVERT: B 54 GLU cc_start: 0.7175 (pm20) cc_final: 0.6960 (pm20) REVERT: B 80 ARG cc_start: 0.8314 (ttp-170) cc_final: 0.8079 (ttp-170) REVERT: B 187 TYR cc_start: 0.8830 (p90) cc_final: 0.8007 (p90) REVERT: C 102 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: D 8 GLU cc_start: 0.8036 (tp30) cc_final: 0.7299 (tp30) REVERT: D 33 ILE cc_start: 0.8453 (mm) cc_final: 0.7910 (mp) REVERT: D 37 LEU cc_start: 0.7672 (mt) cc_final: 0.7464 (mm) REVERT: D 179 PHE cc_start: 0.8754 (t80) cc_final: 0.8471 (t80) outliers start: 21 outliers final: 12 residues processed: 163 average time/residue: 0.1932 time to fit residues: 46.8406 Evaluate side-chains 152 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124779 restraints weight = 15706.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129359 restraints weight = 8990.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132425 restraints weight = 6253.611| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10544 Z= 0.131 Angle : 0.572 8.117 14269 Z= 0.299 Chirality : 0.043 0.167 1605 Planarity : 0.004 0.048 1737 Dihedral : 8.363 82.916 1411 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.23 % Allowed : 16.96 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1235 helix: 1.10 (0.22), residues: 589 sheet: 0.40 (0.35), residues: 207 loop : -1.48 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 31 HIS 0.010 0.001 HIS B 53 PHE 0.033 0.001 PHE D 72 TYR 0.018 0.001 TYR B 63 ARG 0.004 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 498) hydrogen bonds : angle 4.70930 ( 1443) covalent geometry : bond 0.00293 (10544) covalent geometry : angle 0.57249 (14269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.033 Fit side-chains REVERT: A 165 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7743 (pt) REVERT: A 263 ARG cc_start: 0.5562 (ptt-90) cc_final: 0.5213 (ptp90) REVERT: A 315 TYR cc_start: 0.5698 (OUTLIER) cc_final: 0.5011 (t80) REVERT: A 375 LYS cc_start: 0.8513 (tmmt) cc_final: 0.8126 (ttpp) REVERT: B 89 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8338 (ttpp) REVERT: B 187 TYR cc_start: 0.8554 (p90) cc_final: 0.7922 (p90) REVERT: C 33 GLU cc_start: 0.7744 (pm20) cc_final: 0.7543 (pm20) REVERT: C 102 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: C 123 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: C 362 TRP cc_start: 0.7416 (t60) cc_final: 0.6311 (m-90) REVERT: D 8 GLU cc_start: 0.7963 (tp30) cc_final: 0.6765 (tp30) REVERT: D 11 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7675 (ttp80) REVERT: D 12 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7278 (mt0) REVERT: D 47 ILE cc_start: 0.5290 (OUTLIER) cc_final: 0.4887 (mp) REVERT: D 179 PHE cc_start: 0.8680 (t80) cc_final: 0.8324 (t80) outliers start: 25 outliers final: 11 residues processed: 161 average time/residue: 0.1897 time to fit residues: 44.8729 Evaluate side-chains 149 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.0040 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.161226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124901 restraints weight = 15715.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129373 restraints weight = 9009.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132429 restraints weight = 6326.867| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10544 Z= 0.132 Angle : 0.556 7.975 14269 Z= 0.291 Chirality : 0.042 0.163 1605 Planarity : 0.004 0.044 1737 Dihedral : 7.847 78.395 1411 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.77 % Allowed : 18.66 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1235 helix: 1.29 (0.22), residues: 589 sheet: 0.56 (0.37), residues: 199 loop : -1.49 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 31 HIS 0.011 0.001 HIS B 53 PHE 0.024 0.001 PHE D 255 TYR 0.017 0.001 TYR B 150 ARG 0.004 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 498) hydrogen bonds : angle 4.53531 ( 1443) covalent geometry : bond 0.00298 (10544) covalent geometry : angle 0.55593 (14269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.779 Fit side-chains REVERT: A 139 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7650 (tp) REVERT: A 263 ARG cc_start: 0.5615 (ptt-90) cc_final: 0.5238 (ptp90) REVERT: A 375 LYS cc_start: 0.8499 (tmmt) cc_final: 0.8061 (ttpp) REVERT: B 80 ARG cc_start: 0.7967 (ttp-170) cc_final: 0.7155 (ttm170) REVERT: B 89 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8329 (ttpp) REVERT: B 187 TYR cc_start: 0.8568 (p90) cc_final: 0.8004 (p90) REVERT: C 102 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: C 123 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: C 362 TRP cc_start: 0.7431 (t60) cc_final: 0.7032 (t60) REVERT: D 8 GLU cc_start: 0.8004 (tp30) cc_final: 0.6806 (tp30) REVERT: D 11 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7742 (ttp80) REVERT: D 12 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: D 33 ILE cc_start: 0.8515 (mm) cc_final: 0.7864 (mt) REVERT: D 37 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7556 (mm) REVERT: D 47 ILE cc_start: 0.5368 (OUTLIER) cc_final: 0.4989 (mp) REVERT: D 179 PHE cc_start: 0.8584 (t80) cc_final: 0.8178 (t80) outliers start: 31 outliers final: 17 residues processed: 160 average time/residue: 0.2145 time to fit residues: 50.6782 Evaluate side-chains 156 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126214 restraints weight = 15311.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130531 restraints weight = 8789.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133536 restraints weight = 6161.105| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10544 Z= 0.129 Angle : 0.550 7.972 14269 Z= 0.287 Chirality : 0.042 0.175 1605 Planarity : 0.004 0.043 1737 Dihedral : 7.438 75.293 1411 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.12 % Allowed : 18.93 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1235 helix: 1.35 (0.22), residues: 589 sheet: 0.59 (0.37), residues: 200 loop : -1.49 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 31 HIS 0.013 0.001 HIS B 53 PHE 0.018 0.001 PHE D 72 TYR 0.016 0.001 TYR B 63 ARG 0.003 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 498) hydrogen bonds : angle 4.47935 ( 1443) covalent geometry : bond 0.00293 (10544) covalent geometry : angle 0.54966 (14269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 1.047 Fit side-chains REVERT: A 139 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7650 (tp) REVERT: A 263 ARG cc_start: 0.5591 (ptt-90) cc_final: 0.5234 (ptp90) REVERT: A 375 LYS cc_start: 0.8457 (tmmt) cc_final: 0.8092 (ttpp) REVERT: B 80 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7555 (ttp-110) REVERT: B 89 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8332 (ttpp) REVERT: B 144 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8391 (tp) REVERT: B 187 TYR cc_start: 0.8521 (p90) cc_final: 0.7894 (p90) REVERT: C 102 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: C 123 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: D 8 GLU cc_start: 0.7999 (tp30) cc_final: 0.6817 (tp30) REVERT: D 11 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7755 (ttp80) REVERT: D 12 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: D 33 ILE cc_start: 0.8447 (mm) cc_final: 0.8113 (mm) REVERT: D 37 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7618 (mm) REVERT: D 47 ILE cc_start: 0.5426 (OUTLIER) cc_final: 0.5023 (mp) REVERT: D 118 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7824 (tt) REVERT: D 179 PHE cc_start: 0.8538 (t80) cc_final: 0.8148 (t80) outliers start: 35 outliers final: 19 residues processed: 167 average time/residue: 0.1974 time to fit residues: 48.4417 Evaluate side-chains 160 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 8 optimal weight: 0.0470 chunk 119 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.160059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124692 restraints weight = 15562.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129146 restraints weight = 8926.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132120 restraints weight = 6176.492| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10544 Z= 0.146 Angle : 0.566 7.941 14269 Z= 0.295 Chirality : 0.043 0.176 1605 Planarity : 0.004 0.042 1737 Dihedral : 7.284 73.362 1411 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.95 % Allowed : 19.46 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1235 helix: 1.36 (0.22), residues: 589 sheet: 0.61 (0.37), residues: 200 loop : -1.51 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 31 HIS 0.009 0.001 HIS B 53 PHE 0.034 0.001 PHE A 389 TYR 0.018 0.001 TYR B 150 ARG 0.004 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 498) hydrogen bonds : angle 4.46525 ( 1443) covalent geometry : bond 0.00343 (10544) covalent geometry : angle 0.56632 (14269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.255 Fit side-chains REVERT: A 139 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7642 (tp) REVERT: A 184 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7971 (mt) REVERT: A 263 ARG cc_start: 0.5614 (ptt-90) cc_final: 0.5206 (ptp90) REVERT: B 89 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8335 (ttpp) REVERT: B 187 TYR cc_start: 0.8557 (p90) cc_final: 0.7940 (p90) REVERT: C 102 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: C 123 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: C 236 MET cc_start: 0.7847 (mmt) cc_final: 0.7617 (mmm) REVERT: D 8 GLU cc_start: 0.8025 (tp30) cc_final: 0.6948 (tp30) REVERT: D 12 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: D 33 ILE cc_start: 0.8440 (mm) cc_final: 0.8128 (mm) REVERT: D 37 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7587 (mm) REVERT: D 47 ILE cc_start: 0.5471 (OUTLIER) cc_final: 0.5085 (mp) REVERT: D 80 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8122 (mtm180) REVERT: D 179 PHE cc_start: 0.8543 (t80) cc_final: 0.8180 (t80) outliers start: 33 outliers final: 21 residues processed: 161 average time/residue: 0.2301 time to fit residues: 54.6060 Evaluate side-chains 160 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 0.3980 chunk 20 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 177 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 = 0.3957 r_free = 0.3957 target = 0.159776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123211 restraints weight = 15862.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127675 restraints weight = 9124.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130748 restraints weight = 6428.465| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10544 Z= 0.164 Angle : 0.582 7.852 14269 Z= 0.305 Chirality : 0.043 0.179 1605 Planarity : 0.004 0.044 1737 Dihedral : 7.232 75.540 1411 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.39 % Allowed : 19.73 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1235 helix: 1.32 (0.22), residues: 590 sheet: 0.62 (0.37), residues: 200 loop : -1.59 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 31 HIS 0.007 0.001 HIS B 53 PHE 0.018 0.001 PHE A 281 TYR 0.019 0.001 TYR B 150 ARG 0.009 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 498) hydrogen bonds : angle 4.51034 ( 1443) covalent geometry : bond 0.00390 (10544) covalent geometry : angle 0.58211 (14269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.250 Fit side-chains REVERT: A 184 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7996 (mt) REVERT: A 263 ARG cc_start: 0.5457 (ptt-90) cc_final: 0.5044 (ptp90) REVERT: A 284 LEU cc_start: 0.5298 (OUTLIER) cc_final: 0.4945 (tt) REVERT: A 315 TYR cc_start: 0.5968 (OUTLIER) cc_final: 0.5766 (t80) REVERT: B 89 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8346 (ttpp) REVERT: B 187 TYR cc_start: 0.8570 (p90) cc_final: 0.7889 (p90) REVERT: C 102 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: C 123 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: C 362 TRP cc_start: 0.7273 (t60) cc_final: 0.6287 (m100) REVERT: D 11 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8018 (ttm-80) REVERT: D 12 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: D 33 ILE cc_start: 0.8464 (mm) cc_final: 0.8150 (mm) REVERT: D 37 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7619 (mm) REVERT: D 47 ILE cc_start: 0.5611 (OUTLIER) cc_final: 0.5180 (mp) REVERT: D 80 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8113 (mtm180) REVERT: D 179 PHE cc_start: 0.8562 (t80) cc_final: 0.8211 (t80) outliers start: 38 outliers final: 21 residues processed: 162 average time/residue: 0.2361 time to fit residues: 56.0396 Evaluate side-chains 164 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 67 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 93 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 177 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 = 0.3969 r_free = 0.3969 target = 0.160649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124679 restraints weight = 15833.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129056 restraints weight = 9271.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132049 restraints weight = 6565.302| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10544 Z= 0.142 Angle : 0.567 7.944 14269 Z= 0.295 Chirality : 0.043 0.190 1605 Planarity : 0.004 0.044 1737 Dihedral : 7.070 76.929 1411 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.68 % Allowed : 20.18 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1235 helix: 1.40 (0.22), residues: 589 sheet: 0.67 (0.38), residues: 200 loop : -1.56 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 31 HIS 0.020 0.001 HIS B 53 PHE 0.028 0.001 PHE A 389 TYR 0.016 0.001 TYR C 391 ARG 0.006 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 498) hydrogen bonds : angle 4.43277 ( 1443) covalent geometry : bond 0.00331 (10544) covalent geometry : angle 0.56727 (14269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.315 Fit side-chains REVERT: A 263 ARG cc_start: 0.5439 (ptt-90) cc_final: 0.5042 (ptp90) REVERT: B 89 LYS cc_start: 0.8829 (ttmt) cc_final: 0.8346 (ttpp) REVERT: B 187 TYR cc_start: 0.8525 (p90) cc_final: 0.7851 (p90) REVERT: C 102 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: C 123 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: C 362 TRP cc_start: 0.7278 (t60) cc_final: 0.6159 (m-90) REVERT: D 11 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: D 12 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: D 33 ILE cc_start: 0.8453 (mm) cc_final: 0.8127 (mm) REVERT: D 37 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7618 (mm) REVERT: D 47 ILE cc_start: 0.5681 (OUTLIER) cc_final: 0.5200 (mp) REVERT: D 80 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8158 (mtm180) outliers start: 30 outliers final: 24 residues processed: 155 average time/residue: 0.2158 time to fit residues: 49.3719 Evaluate side-chains 160 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN ** D 177 GLN ** 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 = 0.3944 r_free = 0.3944 target = 0.158788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123476 restraints weight = 15585.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127675 restraints weight = 9038.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130573 restraints weight = 6377.119| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10544 Z= 0.172 Angle : 0.597 8.064 14269 Z= 0.312 Chirality : 0.043 0.193 1605 Planarity : 0.004 0.045 1737 Dihedral : 7.088 81.535 1411 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.95 % Allowed : 20.36 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1235 helix: 1.33 (0.22), residues: 590 sheet: 0.68 (0.37), residues: 199 loop : -1.64 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 31 HIS 0.019 0.001 HIS B 53 PHE 0.017 0.001 PHE B 74 TYR 0.019 0.001 TYR B 150 ARG 0.006 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 498) hydrogen bonds : angle 4.49981 ( 1443) covalent geometry : bond 0.00411 (10544) covalent geometry : angle 0.59747 (14269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.058 Fit side-chains REVERT: A 184 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7996 (mt) REVERT: A 263 ARG cc_start: 0.5499 (ptt-90) cc_final: 0.5090 (ptp90) REVERT: A 284 LEU cc_start: 0.5579 (OUTLIER) cc_final: 0.5159 (tt) REVERT: A 315 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5674 (t80) REVERT: B 89 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8350 (ttpp) REVERT: B 187 TYR cc_start: 0.8547 (p90) cc_final: 0.7834 (p90) REVERT: C 102 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8131 (pm20) REVERT: C 123 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: C 362 TRP cc_start: 0.7271 (t60) cc_final: 0.7016 (t60) REVERT: D 11 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7961 (ttm-80) REVERT: D 12 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: D 33 ILE cc_start: 0.8420 (mm) cc_final: 0.8089 (mm) REVERT: D 37 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7556 (mm) REVERT: D 47 ILE cc_start: 0.5826 (OUTLIER) cc_final: 0.5328 (mp) REVERT: D 80 ARG cc_start: 0.8556 (ttp80) cc_final: 0.8208 (mtm180) outliers start: 33 outliers final: 23 residues processed: 152 average time/residue: 0.2376 time to fit residues: 53.0686 Evaluate side-chains 166 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 177 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 = 0.3962 r_free = 0.3962 target = 0.160005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124691 restraints weight = 15391.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128993 restraints weight = 8873.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131916 restraints weight = 6220.957| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10544 Z= 0.138 Angle : 0.570 8.047 14269 Z= 0.297 Chirality : 0.043 0.196 1605 Planarity : 0.004 0.045 1737 Dihedral : 6.994 81.937 1411 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.95 % Allowed : 20.27 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1235 helix: 1.42 (0.22), residues: 589 sheet: 0.73 (0.37), residues: 199 loop : -1.63 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 31 HIS 0.018 0.001 HIS B 53 PHE 0.031 0.001 PHE D 179 TYR 0.017 0.001 TYR C 391 ARG 0.006 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 498) hydrogen bonds : angle 4.43223 ( 1443) covalent geometry : bond 0.00321 (10544) covalent geometry : angle 0.57004 (14269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3761.99 seconds wall clock time: 68 minutes 31.33 seconds (4111.33 seconds total)