Starting phenix.real_space_refine on Fri Aug 7 07:20:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9smr_55040/08_2026/9smr_55040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9smr_55040/08_2026/9smr_55040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9smr_55040/08_2026/9smr_55040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9smr_55040/08_2026/9smr_55040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9smr_55040/08_2026/9smr_55040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9smr_55040/08_2026/9smr_55040.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 120 5.16 5 C 12449 2.51 5 N 3297 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19528 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2480 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 6, 'TRANS': 302} Chain breaks: 2 Chain: "B" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2079 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 2 Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3060 Classifications: {'peptide': 381} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 352} Chain: "D" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1889 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain: "E" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 7, 'TRANS': 50} Chain: "F" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2060 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 4, 'TRANS': 253} Chain: "G" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2057 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 2 Chain: "H" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3078 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 354} Chain: "J" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 7, 'TRANS': 50} Chain: "I" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1889 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.23, per 1000 atoms: 0.22 Number of scatterers: 19528 At special positions: 0 Unit cell: (100.907, 132.839, 232.469, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 120 16.00 O 3660 8.00 N 3297 7.00 C 12449 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: 1.63 Conformation dependent library (CDL) restraints added in 700.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 124 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 122 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 124 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 122 " 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4636 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 40.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 111 through 126 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.698A pdb=" N HIS A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 269 removed outlier: 3.554A pdb=" N HIS A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 93 through 112 removed outlier: 3.537A pdb=" N LEU B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 146 removed outlier: 3.660A pdb=" N MET B 145 " --> pdb=" O MET B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 252 removed outlier: 3.753A pdb=" N LEU B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 257 through 279 Processing helix chain 'B' and resid 279 through 314 removed outlier: 3.585A pdb=" N LEU B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 14 through 25 removed outlier: 3.683A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 112 through 134 removed outlier: 4.045A pdb=" N GLU C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 148 removed outlier: 3.673A pdb=" N GLU C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 249 through 282 Processing helix chain 'C' and resid 357 through 381 Proline residue: C 371 - end of helix Processing helix chain 'D' and resid 119 through 139 removed outlier: 3.515A pdb=" N VAL D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 removed outlier: 4.006A pdb=" N LEU D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 229 through 238 Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.662A pdb=" N PHE D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET D 268 " --> pdb=" O MET D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 removed outlier: 3.778A pdb=" N LEU D 291 " --> pdb=" O PRO D 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 313 removed outlier: 4.073A pdb=" N LYS E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 111 through 117 Processing helix chain 'F' and resid 118 through 125 Processing helix chain 'F' and resid 188 through 198 Processing helix chain 'F' and resid 211 through 259 removed outlier: 4.474A pdb=" N GLU F 217 " --> pdb=" O HIS F 213 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET F 218 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 94 through 97 Processing helix chain 'G' and resid 98 through 112 removed outlier: 4.002A pdb=" N THR G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 146 removed outlier: 3.885A pdb=" N MET G 145 " --> pdb=" O MET G 141 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP G 146 " --> pdb=" O TYR G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 230 Processing helix chain 'G' and resid 233 through 252 removed outlier: 3.925A pdb=" N LYS G 237 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 279 Processing helix chain 'G' and resid 279 through 316 Processing helix chain 'H' and resid 2 through 10 Processing helix chain 'H' and resid 14 through 25 removed outlier: 3.656A pdb=" N ILE H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY H 25 " --> pdb=" O VAL H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 111 through 133 removed outlier: 3.588A pdb=" N GLN H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 148 removed outlier: 4.016A pdb=" N GLU H 148 " --> pdb=" O THR H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 154 removed outlier: 3.656A pdb=" N ASN H 154 " --> pdb=" O GLN H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 229 Processing helix chain 'H' and resid 248 through 283 removed outlier: 4.137A pdb=" N GLN H 252 " --> pdb=" O ASP H 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 253 " --> pdb=" O TYR H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 378 Proline residue: H 371 - end of helix removed outlier: 3.712A pdb=" N PHE H 378 " --> pdb=" O GLN H 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 313 removed outlier: 4.465A pdb=" N LYS J 294 " --> pdb=" O ASN J 290 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL J 295 " --> pdb=" O GLN J 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 139 removed outlier: 3.695A pdb=" N VAL I 123 " --> pdb=" O ASN I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 172 removed outlier: 4.504A pdb=" N LEU I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS I 169 " --> pdb=" O GLU I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 191 removed outlier: 3.813A pdb=" N LEU I 186 " --> pdb=" O ASN I 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE I 187 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN I 191 " --> pdb=" O PHE I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 238 Processing helix chain 'I' and resid 262 through 272 removed outlier: 3.715A pdb=" N ASP I 272 " --> pdb=" O MET I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 299 removed outlier: 3.702A pdb=" N LEU I 291 " --> pdb=" O PRO I 287 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU I 298 " --> pdb=" O CYS I 294 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU I 299 " --> pdb=" O MET I 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 169 removed outlier: 6.627A pdb=" N ALA A 8 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA A 169 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 10 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER A 11 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LYS A 63 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 34 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 64 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE A 32 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLU A 30 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY A 35 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL A 96 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N VAL A 131 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A 97 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LEU A 133 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP A 99 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU A 135 " --> pdb=" O TRP A 99 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 101 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169 removed outlier: 6.627A pdb=" N ALA A 8 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA A 169 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 10 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER A 11 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LYS A 63 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 34 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 64 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE A 32 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLU A 30 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY A 35 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL A 96 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N VAL A 131 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A 97 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LEU A 133 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP A 99 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU A 135 " --> pdb=" O TRP A 99 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 101 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE B 158 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 169 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N CYS B 156 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR B 171 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE B 154 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE B 173 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU B 152 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER B 175 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N VAL B 150 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS B 124 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL B 117 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY B 40 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 119 " --> pdb=" O CYS B 38 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N MET B 35 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU B 41 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE B 74 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER B 76 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 12 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 219 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 14 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 300 removed outlier: 6.722A pdb=" N VAL D 82 " --> pdb=" O ASN E 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 36 through 42 removed outlier: 3.764A pdb=" N ARG C 36 " --> pdb=" O HIS C 59 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU C 40 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG C 55 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N SER C 42 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS C 53 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 155 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AA7, first strand: chain 'C' and resid 286 through 289 removed outlier: 6.815A pdb=" N THR C 298 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR C 289 " --> pdb=" O LYS C 296 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LYS C 296 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N CYS C 307 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 330 " --> pdb=" O CYS C 307 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR C 340 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N TYR C 331 " --> pdb=" O GLN C 338 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N GLN C 338 " --> pdb=" O TYR C 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 153 through 160 removed outlier: 6.178A pdb=" N LEU D 146 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLY D 158 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE D 144 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL D 95 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VAL D 147 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE D 97 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL D 149 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU D 99 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG D 212 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 214 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 211 " --> pdb=" O PHE D 242 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASP D 244 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR D 213 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL D 246 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU D 215 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE D 248 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TYR D 217 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 166 through 169 removed outlier: 7.716A pdb=" N ILE F 59 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA F 8 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE F 61 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU F 10 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LYS F 63 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN F 62 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU F 34 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR F 64 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE F 32 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLU F 30 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY F 35 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL F 96 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY G 166 " --> pdb=" O HIS F 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 166 through 169 removed outlier: 7.716A pdb=" N ILE F 59 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA F 8 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE F 61 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU F 10 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LYS F 63 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN F 62 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU F 34 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR F 64 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE F 32 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLU F 30 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY F 35 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL F 96 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY G 166 " --> pdb=" O HIS F 151 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG G 167 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE G 157 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL G 150 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N CYS G 38 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP G 120 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY G 36 " --> pdb=" O TRP G 120 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N MET G 35 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE G 79 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU G 37 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL G 77 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE G 39 " --> pdb=" O HIS G 75 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA G 11 " --> pdb=" O VAL G 72 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE G 74 " --> pdb=" O ALA G 11 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS G 13 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N SER G 76 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLU G 15 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N ILE G 78 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL G 12 " --> pdb=" O HIS G 217 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL G 219 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU G 14 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 36 through 41 removed outlier: 4.574A pdb=" N LEU H 40 " --> pdb=" O ARG H 55 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG H 55 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP H 83 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 155 through 156 Processing sheet with id=AB4, first strand: chain 'H' and resid 286 through 289 removed outlier: 6.456A pdb=" N THR H 298 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR H 289 " --> pdb=" O LYS H 296 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS H 296 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 153 through 155 removed outlier: 3.572A pdb=" N GLU I 143 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA I 145 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG I 212 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE I 214 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS I 98 " --> pdb=" O ILE I 214 " (cutoff:3.500A) 983 hydrogen bonds defined for protein. 2841 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: 3.57 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5640 1.33 - 1.45: 3154 1.45 - 1.57: 11000 1.57 - 1.69: 2 1.69 - 1.81: 177 Bond restraints: 19973 Sorted by residual: bond pdb=" C LYS B 87 " pdb=" N ASP B 88 " ideal model delta sigma weight residual 1.330 1.497 -0.167 1.29e-02 6.01e+03 1.67e+02 bond pdb=" C ASP B 88 " pdb=" N ARG B 89 " ideal model delta sigma weight residual 1.333 1.425 -0.093 1.38e-02 5.25e+03 4.53e+01 bond pdb=" C GLY G 119 " pdb=" N TRP G 120 " ideal model delta sigma weight residual 1.329 1.263 0.066 1.36e-02 5.41e+03 2.36e+01 bond pdb=" C VAL B 136 " pdb=" N ARG B 137 " ideal model delta sigma weight residual 1.334 1.394 -0.059 1.27e-02 6.20e+03 2.19e+01 bond pdb=" CA TRP B 120 " pdb=" CB TRP B 120 " ideal model delta sigma weight residual 1.532 1.456 0.076 1.74e-02 3.30e+03 1.89e+01 ... (remaining 19968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 26362 2.27 - 4.53: 583 4.53 - 6.80: 75 6.80 - 9.06: 11 9.06 - 11.33: 8 Bond angle restraints: 27039 Sorted by residual: angle pdb=" CA ASP G 135 " pdb=" CB ASP G 135 " pdb=" CG ASP G 135 " ideal model delta sigma weight residual 112.60 122.02 -9.42 1.00e+00 1.00e+00 8.87e+01 angle pdb=" N PRO H 49 " pdb=" CA PRO H 49 " pdb=" C PRO H 49 " ideal model delta sigma weight residual 113.53 124.86 -11.33 1.39e+00 5.18e-01 6.64e+01 angle pdb=" O LYS B 87 " pdb=" C LYS B 87 " pdb=" N ASP B 88 " ideal model delta sigma weight residual 122.87 132.04 -9.17 1.23e+00 6.61e-01 5.55e+01 angle pdb=" C GLU I 258 " pdb=" CA GLU I 258 " pdb=" CB GLU I 258 " ideal model delta sigma weight residual 116.54 108.21 8.33 1.15e+00 7.56e-01 5.24e+01 angle pdb=" N PRO H 51 " pdb=" CA PRO H 51 " pdb=" CB PRO H 51 " ideal model delta sigma weight residual 103.25 95.88 7.37 1.05e+00 9.07e-01 4.92e+01 ... (remaining 27034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11182 17.97 - 35.94: 714 35.94 - 53.91: 138 53.91 - 71.88: 58 71.88 - 89.85: 8 Dihedral angle restraints: 12100 sinusoidal: 4957 harmonic: 7143 Sorted by residual: dihedral pdb=" CA TYR B 121 " pdb=" C TYR B 121 " pdb=" N HIS B 122 " pdb=" CA HIS B 122 " ideal model delta harmonic sigma weight residual 180.00 150.84 29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PRO G 131 " pdb=" C PRO G 131 " pdb=" N SER G 132 " pdb=" CA SER G 132 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA TYR G 121 " pdb=" C TYR G 121 " pdb=" N HIS G 122 " pdb=" CA HIS G 122 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 12097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2644 0.071 - 0.141: 331 0.141 - 0.212: 12 0.212 - 0.282: 1 0.282 - 0.353: 1 Chirality restraints: 2989 Sorted by residual: chirality pdb=" CA PRO H 49 " pdb=" N PRO H 49 " pdb=" C PRO H 49 " pdb=" CB PRO H 49 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA TYR B 121 " pdb=" N TYR B 121 " pdb=" C TYR B 121 " pdb=" CB TYR B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE F 139 " pdb=" N ILE F 139 " pdb=" C ILE F 139 " pdb=" CB ILE F 139 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2986 not shown) Planarity restraints: 3493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 119 " -0.029 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C GLY G 119 " 0.100 2.00e-02 2.50e+03 pdb=" O GLY G 119 " -0.037 2.00e-02 2.50e+03 pdb=" N TRP G 120 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 123 " 0.027 2.00e-02 2.50e+03 5.37e-02 2.89e+01 pdb=" C GLN H 123 " -0.093 2.00e-02 2.50e+03 pdb=" O GLN H 123 " 0.034 2.00e-02 2.50e+03 pdb=" N TYR H 124 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 120 " 0.054 2.00e-02 2.50e+03 3.20e-02 2.57e+01 pdb=" CG TRP B 120 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 120 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 120 " -0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP B 120 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP B 120 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 120 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 120 " 0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 120 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 120 " 0.039 2.00e-02 2.50e+03 ... (remaining 3490 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 24 2.60 - 3.17: 17193 3.17 - 3.75: 29600 3.75 - 4.32: 41735 4.32 - 4.90: 68078 Nonbonded interactions: 156630 Sorted by model distance: nonbonded pdb=" OD2 ASP B 135 " pdb="ZN ZN B 401 " model vdw 2.024 2.230 nonbonded pdb=" OD2 ASP G 135 " pdb="ZN ZN G 401 " model vdw 2.056 2.230 nonbonded pdb="ZN ZN G 401 " pdb=" O HOH G 501 " model vdw 2.116 2.230 nonbonded pdb=" OD1 ASP B 88 " pdb=" O HOH B 501 " model vdw 2.275 3.040 nonbonded pdb=" O ASP A 60 " pdb=" OD1 ASP A 60 " model vdw 2.417 3.040 ... (remaining 156625 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 'B' and (resid 8 through 43 or resid 69 through 206 or resid 208 through \ 401)) selection = chain 'G' } ncs_group { reference = chain 'C' selection = (chain 'H' and resid 1 through 381) } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.310 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.007 0.793 19977 Z= 0.334 Angle : 0.790 11.328 27039 Z= 0.503 Chirality : 0.045 0.353 2989 Planarity : 0.010 0.190 3493 Dihedral : 13.017 89.847 7464 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 1.28 % Allowed : 7.19 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2404 helix: 0.39 (0.17), residues: 936 sheet: -0.82 (0.26), residues: 421 loop : -1.81 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG D 133 TYR 0.028 0.002 TYR C 268 PHE 0.018 0.002 PHE B 154 TRP 0.054 0.004 TRP B 120 HIS 0.028 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.27 (19973) covalent geometry : angle 0.79049 / 0.50 (27039) hydrogen bonds : bond 0.13322 / 8.59 ( 920) hydrogen bonds : angle 6.69387 / 4.86 ( 2841) metal coordination : bond 0.41382 / 23.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8899 (mt) cc_final: 0.8442 (mt) REVERT: A 224 GLU cc_start: 0.9214 (tt0) cc_final: 0.8899 (tp30) REVERT: A 299 MET cc_start: 0.6010 (mtp) cc_final: 0.5543 (ttm) REVERT: A 303 ASN cc_start: 0.8240 (m-40) cc_final: 0.8012 (m-40) REVERT: A 305 HIS cc_start: 0.8852 (m90) cc_final: 0.8119 (m-70) REVERT: B 88 ASP cc_start: 0.7706 (m-30) cc_final: 0.6805 (t0) REVERT: B 162 ASN cc_start: 0.8221 (m-40) cc_final: 0.7935 (m-40) REVERT: C 139 MET cc_start: 0.8378 (tpt) cc_final: 0.7791 (tpp) REVERT: C 155 MET cc_start: 0.8316 (mtp) cc_final: 0.8096 (mtp) REVERT: D 128 ILE cc_start: 0.8861 (mm) cc_final: 0.8624 (mm) REVERT: D 268 MET cc_start: 0.6511 (mpt) cc_final: 0.6310 (mpt) REVERT: H 1 MET cc_start: 0.6164 (mmt) cc_final: 0.5189 (tpp) REVERT: J 304 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8729 (pt0) outliers start: 28 outliers final: 3 residues processed: 291 average time/residue: 0.1668 time to fit residues: 72.3361 Evaluate side-chains 159 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain F residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 235 optimal weight: 30.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 GLN B 162 ASN B 217 HIS B 275 GLN B 294 ASN C 123 GLN D 83 GLN ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 HIS G 75 HIS G 263 HIS H 311 HIS H 344 GLN I 125 GLN I 136 HIS I 249 HIS ** I 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.118187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.077664 restraints weight = 65478.917| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 4.93 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19977 Z= 0.170 Angle : 0.618 8.528 27039 Z= 0.323 Chirality : 0.042 0.179 2989 Planarity : 0.005 0.062 3493 Dihedral : 4.295 58.079 2616 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.09 % Allowed : 9.11 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2404 helix: 1.86 (0.17), residues: 942 sheet: -0.16 (0.27), residues: 397 loop : -1.48 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 164 TYR 0.015 0.002 TYR E 303 PHE 0.024 0.002 PHE J 320 TRP 0.027 0.002 TRP D 155 HIS 0.006 0.001 HIS I 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (19973) covalent geometry : angle 0.61812 / 0.32 (27039) hydrogen bonds : bond 0.05392 / 3.57 ( 920) hydrogen bonds : angle 5.14917 / 3.73 ( 2841) metal coordination : bond 0.01600 / 0.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6446 (mpp) cc_final: 0.6113 (mpp) REVERT: A 224 GLU cc_start: 0.8877 (tt0) cc_final: 0.8632 (tp30) REVERT: A 303 ASN cc_start: 0.7804 (m-40) cc_final: 0.7493 (m-40) REVERT: B 309 MET cc_start: 0.8222 (mmt) cc_final: 0.7730 (tmm) REVERT: C 13 MET cc_start: 0.8579 (mmm) cc_final: 0.8279 (tpt) REVERT: C 155 MET cc_start: 0.7724 (mtp) cc_final: 0.7455 (mtp) REVERT: C 209 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.6913 (t0) REVERT: D 175 THR cc_start: 0.5775 (OUTLIER) cc_final: 0.5477 (m) REVERT: D 232 MET cc_start: 0.6659 (mmp) cc_final: 0.6075 (mmm) REVERT: G 115 MET cc_start: 0.7506 (mtm) cc_final: 0.7150 (mpp) REVERT: H 1 MET cc_start: 0.6020 (mmt) cc_final: 0.5118 (tpp) REVERT: H 187 TYR cc_start: 0.8559 (t80) cc_final: 0.8324 (t80) REVERT: I 130 MET cc_start: 0.1119 (OUTLIER) cc_final: 0.0427 (mtt) REVERT: I 264 MET cc_start: 0.0465 (OUTLIER) cc_final: 0.0074 (mtt) outliers start: 46 outliers final: 22 residues processed: 196 average time/residue: 0.1482 time to fit residues: 45.4270 Evaluate side-chains 164 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 264 MET Chi-restraints excluded: chain I residue 274 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 187 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 234 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS H 8 ASN H 266 GLN J 304 GLN ** J 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 HIS ** I 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.117522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.077039 restraints weight = 65283.520| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 4.81 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19977 Z= 0.154 Angle : 0.570 9.992 27039 Z= 0.295 Chirality : 0.041 0.150 2989 Planarity : 0.004 0.073 3493 Dihedral : 4.264 58.506 2615 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.78 % Allowed : 10.75 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2404 helix: 2.20 (0.17), residues: 944 sheet: -0.03 (0.26), residues: 417 loop : -1.43 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 164 TYR 0.016 0.001 TYR E 303 PHE 0.018 0.002 PHE D 265 TRP 0.016 0.001 TRP H 353 HIS 0.006 0.001 HIS G 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (19973) covalent geometry : angle 0.56994 / 0.30 (27039) hydrogen bonds : bond 0.04889 / 3.23 ( 920) hydrogen bonds : angle 4.76604 / 3.45 ( 2841) metal coordination : bond 0.00348 / 0.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8714 (tp) REVERT: B 109 GLU cc_start: 0.8782 (pp20) cc_final: 0.8509 (pp20) REVERT: B 309 MET cc_start: 0.8208 (mmt) cc_final: 0.7895 (tmm) REVERT: C 13 MET cc_start: 0.8542 (mmm) cc_final: 0.8283 (tpt) REVERT: C 139 MET cc_start: 0.8191 (tpp) cc_final: 0.7919 (tpp) REVERT: C 174 LEU cc_start: 0.8633 (tp) cc_final: 0.8326 (tt) REVERT: C 302 MET cc_start: 0.7230 (ttt) cc_final: 0.6348 (ttt) REVERT: D 263 ASP cc_start: 0.8394 (t0) cc_final: 0.7956 (t0) REVERT: F 29 THR cc_start: 0.6885 (OUTLIER) cc_final: 0.6278 (p) REVERT: G 115 MET cc_start: 0.7733 (mtm) cc_final: 0.7104 (mpp) REVERT: H 1 MET cc_start: 0.5726 (mmt) cc_final: 0.4813 (tpp) outliers start: 39 outliers final: 21 residues processed: 178 average time/residue: 0.1414 time to fit residues: 40.1627 Evaluate side-chains 158 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 274 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 123 optimal weight: 0.6980 chunk 92 optimal weight: 0.0470 chunk 190 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 231 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN B 143 GLN ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS G 96 GLN ** I 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.117448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.077378 restraints weight = 65592.338| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 5.14 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19977 Z= 0.130 Angle : 0.543 11.473 27039 Z= 0.280 Chirality : 0.040 0.147 2989 Planarity : 0.004 0.052 3493 Dihedral : 4.193 58.508 2615 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.91 % Allowed : 11.52 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2404 helix: 2.30 (0.17), residues: 945 sheet: 0.09 (0.26), residues: 396 loop : -1.31 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 164 TYR 0.014 0.001 TYR E 303 PHE 0.016 0.001 PHE C 306 TRP 0.012 0.001 TRP A 99 HIS 0.008 0.001 HIS G 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (19973) covalent geometry : angle 0.54275 / 0.28 (27039) hydrogen bonds : bond 0.04557 / 3.01 ( 920) hydrogen bonds : angle 4.51302 / 3.27 ( 2841) metal coordination : bond 0.00343 / 0.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6411 (mpp) cc_final: 0.6102 (mpp) REVERT: A 243 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8732 (tp) REVERT: B 109 GLU cc_start: 0.8738 (pp20) cc_final: 0.8417 (pp20) REVERT: B 309 MET cc_start: 0.8358 (mmt) cc_final: 0.8055 (tmm) REVERT: C 133 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8467 (tpm170) REVERT: C 139 MET cc_start: 0.8220 (tpp) cc_final: 0.7837 (tpp) REVERT: C 174 LEU cc_start: 0.8640 (tp) cc_final: 0.8295 (tt) REVERT: C 209 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7344 (t0) REVERT: D 139 ASP cc_start: 0.7833 (t0) cc_final: 0.7333 (t0) REVERT: D 172 ASP cc_start: 0.8794 (m-30) cc_final: 0.8055 (p0) REVERT: F 29 THR cc_start: 0.6859 (OUTLIER) cc_final: 0.6264 (p) REVERT: F 145 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7132 (m) REVERT: G 77 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8769 (t) REVERT: G 115 MET cc_start: 0.7750 (mtm) cc_final: 0.6971 (mpp) REVERT: H 1 MET cc_start: 0.5707 (mmt) cc_final: 0.4713 (tpp) REVERT: H 174 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8949 (mm) REVERT: I 130 MET cc_start: 0.1128 (tpp) cc_final: 0.0441 (mtt) outliers start: 42 outliers final: 24 residues processed: 173 average time/residue: 0.1371 time to fit residues: 37.2860 Evaluate side-chains 163 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 255 HIS Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 274 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 35 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 154 optimal weight: 0.0010 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN H 128 GLN J 304 GLN I 301 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.117324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.075724 restraints weight = 64913.735| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 5.12 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19977 Z= 0.160 Angle : 0.551 12.755 27039 Z= 0.284 Chirality : 0.041 0.149 2989 Planarity : 0.004 0.054 3493 Dihedral : 4.239 63.098 2615 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.05 % Allowed : 11.75 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.17), residues: 2404 helix: 2.29 (0.17), residues: 945 sheet: 0.13 (0.26), residues: 393 loop : -1.26 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 164 TYR 0.015 0.001 TYR E 303 PHE 0.018 0.001 PHE C 369 TRP 0.013 0.001 TRP A 99 HIS 0.009 0.001 HIS I 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (19973) covalent geometry : angle 0.55062 / 0.28 (27039) hydrogen bonds : bond 0.04611 / 3.03 ( 920) hydrogen bonds : angle 4.48508 / 3.25 ( 2841) metal coordination : bond 0.00534 / 0.31 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8600 (tp) REVERT: B 309 MET cc_start: 0.8426 (mmt) cc_final: 0.8193 (tmm) REVERT: C 13 MET cc_start: 0.8649 (mmm) cc_final: 0.8392 (tpt) REVERT: C 133 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8455 (tpm170) REVERT: C 139 MET cc_start: 0.8321 (tpp) cc_final: 0.7964 (tpp) REVERT: C 174 LEU cc_start: 0.8591 (tp) cc_final: 0.8203 (tt) REVERT: C 209 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7508 (t0) REVERT: D 139 ASP cc_start: 0.7821 (t0) cc_final: 0.7348 (t0) REVERT: D 237 GLN cc_start: 0.8851 (tp40) cc_final: 0.8640 (mm-40) REVERT: F 29 THR cc_start: 0.6665 (OUTLIER) cc_final: 0.6048 (p) REVERT: F 145 SER cc_start: 0.7756 (OUTLIER) cc_final: 0.7263 (m) REVERT: G 35 MET cc_start: 0.8392 (ttp) cc_final: 0.7973 (ptt) REVERT: H 1 MET cc_start: 0.5721 (mmt) cc_final: 0.4755 (tpp) REVERT: H 155 MET cc_start: 0.6755 (tpt) cc_final: 0.6164 (ttt) REVERT: H 174 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8809 (mm) REVERT: I 130 MET cc_start: 0.1484 (tpp) cc_final: 0.0646 (mtt) outliers start: 45 outliers final: 29 residues processed: 172 average time/residue: 0.1319 time to fit residues: 36.5679 Evaluate side-chains 162 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 255 HIS Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 274 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 31 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 221 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS A 303 ASN B 255 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS J 290 ASN J 304 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075320 restraints weight = 64441.472| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.90 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19977 Z= 0.165 Angle : 0.559 12.529 27039 Z= 0.288 Chirality : 0.041 0.164 2989 Planarity : 0.004 0.053 3493 Dihedral : 4.118 66.518 2613 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.00 % Allowed : 12.43 % Favored : 85.56 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.17), residues: 2404 helix: 2.24 (0.17), residues: 949 sheet: 0.23 (0.26), residues: 385 loop : -1.26 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 164 TYR 0.015 0.001 TYR E 303 PHE 0.027 0.001 PHE C 369 TRP 0.013 0.001 TRP A 99 HIS 0.007 0.001 HIS I 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (19973) covalent geometry : angle 0.55895 / 0.29 (27039) hydrogen bonds : bond 0.04585 / 3.03 ( 920) hydrogen bonds : angle 4.46518 / 3.23 ( 2841) metal coordination : bond 0.00533 / 0.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6458 (mpp) cc_final: 0.6170 (mpp) REVERT: A 243 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8643 (tp) REVERT: C 13 MET cc_start: 0.8674 (mmm) cc_final: 0.8257 (tpt) REVERT: C 209 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7446 (t0) REVERT: D 139 ASP cc_start: 0.8003 (t0) cc_final: 0.7528 (t0) REVERT: D 172 ASP cc_start: 0.8948 (m-30) cc_final: 0.8304 (p0) REVERT: D 237 GLN cc_start: 0.8877 (tp40) cc_final: 0.8658 (mm-40) REVERT: E 313 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7209 (tm-30) REVERT: F 29 THR cc_start: 0.6644 (OUTLIER) cc_final: 0.6029 (p) REVERT: F 145 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7384 (m) REVERT: G 35 MET cc_start: 0.8516 (ttp) cc_final: 0.8042 (ptt) REVERT: G 77 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8796 (t) REVERT: H 1 MET cc_start: 0.5803 (mmt) cc_final: 0.4595 (tpp) REVERT: H 155 MET cc_start: 0.6737 (tpt) cc_final: 0.6443 (tpt) REVERT: I 130 MET cc_start: 0.0686 (tpp) cc_final: -0.0135 (mtt) REVERT: I 264 MET cc_start: 0.2076 (mmm) cc_final: 0.1720 (mmm) outliers start: 44 outliers final: 29 residues processed: 164 average time/residue: 0.1352 time to fit residues: 35.7405 Evaluate side-chains 158 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 255 HIS Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 274 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 116 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.116977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.075749 restraints weight = 64865.014| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.81 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19977 Z= 0.150 Angle : 0.552 10.111 27039 Z= 0.283 Chirality : 0.040 0.154 2989 Planarity : 0.004 0.051 3493 Dihedral : 4.075 68.288 2611 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.91 % Allowed : 13.11 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2404 helix: 2.22 (0.17), residues: 951 sheet: 0.28 (0.26), residues: 390 loop : -1.23 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 164 TYR 0.014 0.001 TYR E 303 PHE 0.013 0.001 PHE A 102 TRP 0.011 0.001 TRP A 99 HIS 0.006 0.001 HIS I 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (19973) covalent geometry : angle 0.55204 / 0.28 (27039) hydrogen bonds : bond 0.04498 / 2.96 ( 920) hydrogen bonds : angle 4.41692 / 3.20 ( 2841) metal coordination : bond 0.00450 / 0.26 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6445 (mpp) cc_final: 0.6146 (mpp) REVERT: A 243 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8632 (tp) REVERT: C 133 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8436 (tpm170) REVERT: C 209 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7546 (t0) REVERT: D 139 ASP cc_start: 0.8035 (t0) cc_final: 0.7544 (t0) REVERT: D 237 GLN cc_start: 0.8881 (tp40) cc_final: 0.8644 (mm-40) REVERT: E 313 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7195 (tm-30) REVERT: F 29 THR cc_start: 0.6614 (OUTLIER) cc_final: 0.5994 (p) REVERT: F 145 SER cc_start: 0.7807 (OUTLIER) cc_final: 0.7343 (m) REVERT: G 35 MET cc_start: 0.8533 (ttp) cc_final: 0.8033 (ptt) REVERT: G 77 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8794 (t) REVERT: G 115 MET cc_start: 0.7531 (mtm) cc_final: 0.6853 (mpp) REVERT: H 1 MET cc_start: 0.5733 (mmt) cc_final: 0.4478 (tpp) REVERT: I 127 MET cc_start: 0.2842 (tpp) cc_final: 0.2615 (tpp) outliers start: 42 outliers final: 31 residues processed: 162 average time/residue: 0.1394 time to fit residues: 36.1947 Evaluate side-chains 161 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 255 HIS Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 274 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 42 optimal weight: 1.9990 chunk 129 optimal weight: 0.0370 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 174 optimal weight: 0.0370 chunk 155 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 HIS ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.117611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075842 restraints weight = 65159.610| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 5.02 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19977 Z= 0.131 Angle : 0.560 15.311 27039 Z= 0.284 Chirality : 0.040 0.185 2989 Planarity : 0.004 0.050 3493 Dihedral : 4.042 69.525 2611 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.87 % Allowed : 13.39 % Favored : 84.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2404 helix: 2.27 (0.17), residues: 946 sheet: 0.28 (0.26), residues: 396 loop : -1.20 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 164 TYR 0.013 0.001 TYR E 303 PHE 0.011 0.001 PHE A 102 TRP 0.010 0.001 TRP A 99 HIS 0.015 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (19973) covalent geometry : angle 0.55964 / 0.28 (27039) hydrogen bonds : bond 0.04360 / 2.87 ( 920) hydrogen bonds : angle 4.35430 / 3.15 ( 2841) metal coordination : bond 0.00341 / 0.19 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6361 (mpp) cc_final: 0.6035 (mpp) REVERT: A 243 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8646 (tp) REVERT: C 209 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7558 (t0) REVERT: D 139 ASP cc_start: 0.8020 (t0) cc_final: 0.7520 (t0) REVERT: D 172 ASP cc_start: 0.8977 (m-30) cc_final: 0.8352 (p0) REVERT: D 237 GLN cc_start: 0.8880 (tp40) cc_final: 0.8650 (mm-40) REVERT: D 294 CYS cc_start: 0.7966 (m) cc_final: 0.7137 (m) REVERT: E 312 ARG cc_start: 0.8463 (tpp80) cc_final: 0.8189 (tpm170) REVERT: E 313 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7152 (tm-30) REVERT: F 29 THR cc_start: 0.6473 (OUTLIER) cc_final: 0.5839 (p) REVERT: F 50 MET cc_start: 0.8661 (tmm) cc_final: 0.8277 (ppp) REVERT: F 145 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7214 (m) REVERT: G 35 MET cc_start: 0.8577 (ttp) cc_final: 0.8030 (ptt) REVERT: G 77 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8754 (t) REVERT: G 115 MET cc_start: 0.7517 (mtm) cc_final: 0.6840 (mpp) REVERT: H 1 MET cc_start: 0.5795 (mmt) cc_final: 0.4586 (tpp) REVERT: H 155 MET cc_start: 0.7121 (tpt) cc_final: 0.6743 (ttt) REVERT: I 130 MET cc_start: 0.0574 (tpp) cc_final: -0.0254 (mtt) outliers start: 41 outliers final: 31 residues processed: 162 average time/residue: 0.1336 time to fit residues: 34.5559 Evaluate side-chains 161 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 255 HIS Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain I residue 235 MET Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 274 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 227 optimal weight: 50.0000 chunk 108 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 164 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 230 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 HIS ** 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 = 0.4226 r_free = 0.4226 target = 0.117266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.075076 restraints weight = 64890.052| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 5.07 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19977 Z= 0.156 Angle : 0.573 15.078 27039 Z= 0.293 Chirality : 0.040 0.144 2989 Planarity : 0.004 0.049 3493 Dihedral : 4.075 71.809 2611 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.19 % Allowed : 13.43 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2404 helix: 2.25 (0.17), residues: 944 sheet: 0.29 (0.26), residues: 396 loop : -1.19 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 164 TYR 0.014 0.001 TYR E 303 PHE 0.013 0.001 PHE A 102 TRP 0.011 0.001 TRP A 99 HIS 0.006 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (19973) covalent geometry : angle 0.57310 / 0.29 (27039) hydrogen bonds : bond 0.04447 / 2.94 ( 920) hydrogen bonds : angle 4.37125 / 3.16 ( 2841) metal coordination : bond 0.00493 / 0.28 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6428 (mpp) cc_final: 0.6105 (mpp) REVERT: A 243 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8718 (tp) REVERT: C 209 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7645 (t0) REVERT: D 139 ASP cc_start: 0.8067 (t0) cc_final: 0.7511 (t0) REVERT: D 172 ASP cc_start: 0.9000 (m-30) cc_final: 0.8384 (p0) REVERT: D 237 GLN cc_start: 0.8863 (tp40) cc_final: 0.8560 (mm-40) REVERT: D 281 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8802 (pm20) REVERT: D 294 CYS cc_start: 0.7968 (m) cc_final: 0.7183 (m) REVERT: E 312 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8193 (tpm170) REVERT: E 313 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7197 (tm-30) REVERT: F 29 THR cc_start: 0.6523 (OUTLIER) cc_final: 0.5891 (p) REVERT: F 50 MET cc_start: 0.8758 (tmm) cc_final: 0.8347 (ppp) REVERT: F 145 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7381 (m) REVERT: G 35 MET cc_start: 0.8635 (ttp) cc_final: 0.7871 (ptt) REVERT: G 77 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8742 (t) REVERT: G 115 MET cc_start: 0.7451 (mtm) cc_final: 0.6924 (mtm) REVERT: H 1 MET cc_start: 0.5543 (mmt) cc_final: 0.4233 (tpp) REVERT: H 155 MET cc_start: 0.6935 (tpt) cc_final: 0.6696 (ttt) REVERT: H 227 HIS cc_start: 0.9043 (OUTLIER) cc_final: 0.8842 (p-80) outliers start: 48 outliers final: 36 residues processed: 163 average time/residue: 0.1223 time to fit residues: 32.6256 Evaluate side-chains 169 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 255 HIS Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain I residue 235 MET Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 274 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 135 optimal weight: 0.7980 chunk 168 optimal weight: 0.5980 chunk 78 optimal weight: 0.0370 chunk 47 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 157 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 HIS ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.117819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.076235 restraints weight = 65461.310| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.87 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19977 Z= 0.126 Angle : 0.573 14.602 27039 Z= 0.290 Chirality : 0.040 0.142 2989 Planarity : 0.004 0.050 3493 Dihedral : 4.030 72.474 2611 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.78 % Allowed : 13.80 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2404 helix: 2.25 (0.17), residues: 951 sheet: 0.44 (0.27), residues: 385 loop : -1.15 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 304 TYR 0.012 0.001 TYR E 303 PHE 0.011 0.001 PHE A 102 TRP 0.010 0.001 TRP A 99 HIS 0.004 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (19973) covalent geometry : angle 0.57272 / 0.29 (27039) hydrogen bonds : bond 0.04325 / 2.85 ( 920) hydrogen bonds : angle 4.30471 / 3.12 ( 2841) metal coordination : bond 0.00297 / 0.17 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8635 (tp) REVERT: D 139 ASP cc_start: 0.8033 (t0) cc_final: 0.7478 (t0) REVERT: D 172 ASP cc_start: 0.8995 (m-30) cc_final: 0.8501 (p0) REVERT: D 237 GLN cc_start: 0.8869 (tp40) cc_final: 0.8559 (mm-40) REVERT: D 281 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8496 (mt-10) REVERT: E 312 ARG cc_start: 0.8500 (tpp80) cc_final: 0.8241 (tpm170) REVERT: E 313 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7162 (tm-30) REVERT: F 29 THR cc_start: 0.6486 (OUTLIER) cc_final: 0.5867 (p) REVERT: F 50 MET cc_start: 0.8511 (tmm) cc_final: 0.7950 (ppp) REVERT: F 145 SER cc_start: 0.7718 (OUTLIER) cc_final: 0.7198 (m) REVERT: G 35 MET cc_start: 0.8572 (ttp) cc_final: 0.7868 (ptt) REVERT: G 77 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8755 (t) REVERT: G 115 MET cc_start: 0.7382 (mtm) cc_final: 0.6802 (mtm) REVERT: H 1 MET cc_start: 0.5449 (mmt) cc_final: 0.4231 (tpp) REVERT: I 130 MET cc_start: 0.0029 (tpp) cc_final: -0.0452 (mtt) outliers start: 39 outliers final: 31 residues processed: 159 average time/residue: 0.1152 time to fit residues: 29.7149 Evaluate side-chains 159 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 255 HIS Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain I residue 235 MET Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 274 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 117 optimal weight: 0.0970 chunk 146 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 0.0030 chunk 212 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 HIS ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS G 285 GLN J 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.117975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.075984 restraints weight = 65467.201| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 5.06 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19977 Z= 0.123 Angle : 0.571 13.826 27039 Z= 0.289 Chirality : 0.040 0.154 2989 Planarity : 0.004 0.049 3493 Dihedral : 4.013 73.519 2611 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.82 % Allowed : 13.84 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2404 helix: 2.25 (0.17), residues: 953 sheet: 0.49 (0.27), residues: 385 loop : -1.15 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 304 TYR 0.012 0.001 TYR E 303 PHE 0.012 0.001 PHE A 287 TRP 0.013 0.001 TRP D 261 HIS 0.007 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19973) covalent geometry : angle 0.57117 / 0.29 (27039) hydrogen bonds : bond 0.04258 / 2.80 ( 920) hydrogen bonds : angle 4.27682 / 3.09 ( 2841) metal coordination : bond 0.00298 / 0.17 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5338.63 seconds wall clock time: 92 minutes 21.00 seconds (5541.00 seconds total)