Starting phenix.real_space_refine on Fri Aug 7 19:18:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ydb_39167/08_2026/8ydb_39167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ydb_39167/08_2026/8ydb_39167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ydb_39167/08_2026/8ydb_39167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ydb_39167/08_2026/8ydb_39167.map" model { file = "/net/cci-nas-00/data/ceres_data/8ydb_39167/08_2026/8ydb_39167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ydb_39167/08_2026/8ydb_39167.cif" } resolution = 3.4 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 102 5.49 5 S 119 5.16 5 C 14874 2.51 5 N 4010 2.21 5 O 4775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 23880 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2002 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1287 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 11, 'rna3p_pur': 21, 'rna3p_pyr': 11} Link IDs: {'rna2p': 26, 'rna3p': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2639 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "H" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2621 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain: "G" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2646 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 15, 'TRANS': 309} Chain: "F" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2628 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "E" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2635 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "D" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2409 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "J" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2718 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 322} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "N" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 5.41, per 1000 atoms: 0.23 Number of scatterers: 23880 At special positions: 0 Unit cell: (138.55, 142.8, 161.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 P 102 15.00 O 4775 8.00 N 4010 7.00 C 14874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 43 sheets defined 35.1% alpha, 20.1% beta 32 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 removed outlier: 3.844A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.700A pdb=" N LEU A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 236 through 240 removed outlier: 3.702A pdb=" N LEU A 240 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.664A pdb=" N ILE B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.735A pdb=" N CYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.703A pdb=" N HIS B 76 " --> pdb=" O CYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 123 through 139 removed outlier: 4.505A pdb=" N GLU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N MET B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 40 Processing helix chain 'I' and resid 102 through 106 removed outlier: 3.990A pdb=" N MET I 106 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 129 Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.614A pdb=" N ALA I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 177 removed outlier: 3.580A pdb=" N PHE I 177 " --> pdb=" O SER I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 202 Processing helix chain 'I' and resid 250 through 259 Processing helix chain 'I' and resid 267 through 271 Processing helix chain 'I' and resid 296 through 305 Processing helix chain 'I' and resid 312 through 326 Processing helix chain 'H' and resid 63 through 68 removed outlier: 4.240A pdb=" N GLU H 68 " --> pdb=" O PRO H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 112 through 129 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.675A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.555A pdb=" N TRP H 149 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.674A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.682A pdb=" N ASN H 256 " --> pdb=" O GLN H 252 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.937A pdb=" N TYR H 271 " --> pdb=" O ASP H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 removed outlier: 3.650A pdb=" N ASP H 302 " --> pdb=" O TYR H 298 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG H 303 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 326 Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.756A pdb=" N ILE G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.559A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 153 removed outlier: 3.530A pdb=" N TRP G 149 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS G 153 " --> pdb=" O ARG G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 201 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.533A pdb=" N ASN G 256 " --> pdb=" O GLN G 252 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 removed outlier: 3.866A pdb=" N TYR G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 307 removed outlier: 3.585A pdb=" N LYS G 307 " --> pdb=" O ARG G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 326 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.888A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 112 through 129 Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.695A pdb=" N ALA F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 153 removed outlier: 3.503A pdb=" N TRP F 149 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG F 150 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 250 through 260 removed outlier: 3.648A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 260 " --> pdb=" O ASN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.962A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.623A pdb=" N ARG E 40 " --> pdb=" O PHE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 removed outlier: 4.496A pdb=" N GLU E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.688A pdb=" N ALA E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 153 removed outlier: 3.677A pdb=" N LEU E 148 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP E 149 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 202 Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.733A pdb=" N ALA E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 4.167A pdb=" N TYR E 271 " --> pdb=" O ASP E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.648A pdb=" N ALA D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.542A pdb=" N LEU D 148 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.670A pdb=" N ILE D 254 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.529A pdb=" N TYR D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'J' and resid 2 through 10 Processing helix chain 'J' and resid 15 through 31 removed outlier: 4.098A pdb=" N GLY J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU J 27 " --> pdb=" O TYR J 23 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE J 28 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN J 29 " --> pdb=" O GLU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 94 removed outlier: 3.835A pdb=" N GLY J 91 " --> pdb=" O LYS J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 111 through 122 Processing helix chain 'J' and resid 124 through 134 removed outlier: 4.224A pdb=" N ASN J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 179 Processing helix chain 'J' and resid 191 through 199 removed outlier: 4.038A pdb=" N GLY J 199 " --> pdb=" O ALA J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 206 Processing helix chain 'J' and resid 217 through 221 Processing helix chain 'J' and resid 223 through 230 removed outlier: 3.658A pdb=" N LYS J 230 " --> pdb=" O LYS J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 265 Processing helix chain 'J' and resid 281 through 292 removed outlier: 4.247A pdb=" N VAL J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN J 286 " --> pdb=" O GLU J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 312 removed outlier: 3.580A pdb=" N GLY J 312 " --> pdb=" O LEU J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.537A pdb=" N ILE A 134 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 5 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 144 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.537A pdb=" N ILE A 134 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 10 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N MET A 106 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASN A 12 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 104 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU A 14 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 102 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER A 107 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE A 59 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 109 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU A 57 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLU A 111 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 55 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 113 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASN A 53 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 14.246A pdb=" N VAL A 55 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N LEU A 162 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU A 57 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 160 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 226 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 195 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER A 223 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA A 193 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY A 225 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 removed outlier: 5.972A pdb=" N VAL A 24 " --> pdb=" O ALA J 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 214 through 216 removed outlier: 5.763A pdb=" N ASP A 214 " --> pdb=" O LEU J 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 42 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.804A pdb=" N THR B 91 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 102 removed outlier: 4.181A pdb=" N LEU B 98 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 102 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 158 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA B 142 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 19 through 20 removed outlier: 3.831A pdb=" N SER I 108 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 30 through 35 current: chain 'I' and resid 158 through 163 Processing sheet with id=AB3, first strand: chain 'I' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 90 through 99 current: chain 'I' and resid 242 through 243 Processing sheet with id=AB4, first strand: chain 'I' and resid 50 through 57 removed outlier: 4.569A pdb=" N CYS I 82 " --> pdb=" O VAL I 223 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL I 223 " --> pdb=" O CYS I 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 106 through 109 removed outlier: 3.605A pdb=" N SER H 108 " --> pdb=" O SER H 20 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.826A pdb=" N ILE H 157 " --> pdb=" O LYS H 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.826A pdb=" N ILE H 157 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR H 160 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 50 through 56 Processing sheet with id=AB9, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'H' and resid 260 through 262 Processing sheet with id=AC2, first strand: chain 'G' and resid 20 through 21 Processing sheet with id=AC3, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 30 through 35 current: chain 'G' and resid 157 through 163 removed outlier: 3.521A pdb=" N THR G 160 " --> pdb=" O PHE G 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AC5, first strand: chain 'G' and resid 50 through 56 removed outlier: 4.471A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 227 through 228 removed outlier: 4.529A pdb=" N LYS G 239 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AC8, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.634A pdb=" N ALA G 283 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AD1, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AD2, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AD3, first strand: chain 'F' and resid 50 through 56 removed outlier: 4.527A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 227 through 228 removed outlier: 4.224A pdb=" N LYS F 239 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AD6, first strand: chain 'E' and resid 19 through 21 removed outlier: 3.754A pdb=" N SER E 108 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 35 current: chain 'E' and resid 157 through 163 Processing sheet with id=AD8, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AD9, first strand: chain 'E' and resid 50 through 55 Processing sheet with id=AE1, first strand: chain 'E' and resid 260 through 262 Processing sheet with id=AE2, first strand: chain 'D' and resid 19 through 21 removed outlier: 3.752A pdb=" N SER D 108 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AE4, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.587A pdb=" N ILE D 93 " --> pdb=" O CYS D 213 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AE6, first strand: chain 'J' and resid 35 through 37 Processing sheet with id=AE7, first strand: chain 'J' and resid 301 through 304 853 hydrogen bonds defined for protein. 2286 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6953 1.34 - 1.46: 5322 1.46 - 1.58: 11941 1.58 - 1.70: 202 1.70 - 1.82: 191 Bond restraints: 24609 Sorted by residual: bond pdb=" C1' C T 44 " pdb=" N1 C T 44 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.78e+00 bond pdb=" C3' G N 17 " pdb=" C2' G N 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.28e+00 bond pdb=" C1' DT T 31 " pdb=" N1 DT T 31 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.26e+00 bond pdb=" C3' DT T 28 " pdb=" C2' DT T 28 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.89e+00 bond pdb=" C3' C T 26 " pdb=" C2' C T 26 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.54e+00 ... (remaining 24604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 33097 2.11 - 4.21: 551 4.21 - 6.32: 42 6.32 - 8.42: 3 8.42 - 10.53: 7 Bond angle restraints: 33700 Sorted by residual: angle pdb=" C5 G C 52 " pdb=" C4 G C 52 " pdb=" N3 G C 52 " ideal model delta sigma weight residual 128.60 126.21 2.39 5.00e-01 4.00e+00 2.28e+01 angle pdb=" C1' G C 52 " pdb=" N9 G C 52 " pdb=" C4 G C 52 " ideal model delta sigma weight residual 126.50 132.63 -6.13 1.30e+00 5.92e-01 2.22e+01 angle pdb=" O5' G C 26 " pdb=" C5' G C 26 " pdb=" C4' G C 26 " ideal model delta sigma weight residual 109.40 112.98 -3.58 8.00e-01 1.56e+00 2.01e+01 angle pdb=" O5' C C 16 " pdb=" C5' C C 16 " pdb=" C4' C C 16 " ideal model delta sigma weight residual 109.40 112.95 -3.55 8.00e-01 1.56e+00 1.97e+01 angle pdb=" N9 G C 52 " pdb=" C4 G C 52 " pdb=" N3 G C 52 " ideal model delta sigma weight residual 126.00 128.62 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 33695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 13910 33.17 - 66.35: 907 66.35 - 99.52: 76 99.52 - 132.70: 0 132.70 - 165.87: 1 Dihedral angle restraints: 14894 sinusoidal: 6984 harmonic: 7910 Sorted by residual: dihedral pdb=" O4' U C 42 " pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sinusoidal sigma weight residual 232.00 66.13 165.87 1 1.70e+01 3.46e-03 6.54e+01 dihedral pdb=" O4' C C 16 " pdb=" C1' C C 16 " pdb=" N1 C C 16 " pdb=" C2 C C 16 " ideal model delta sinusoidal sigma weight residual -128.00 -50.55 -77.45 1 1.70e+01 3.46e-03 2.60e+01 dihedral pdb=" CA ASP B 36 " pdb=" C ASP B 36 " pdb=" N LYS B 37 " pdb=" CA LYS B 37 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 14891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2608 0.039 - 0.079: 821 0.079 - 0.118: 217 0.118 - 0.157: 88 0.157 - 0.197: 5 Chirality restraints: 3739 Sorted by residual: chirality pdb=" C1' A C 22 " pdb=" O4' A C 22 " pdb=" C2' A C 22 " pdb=" N9 A C 22 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" C3' G C 41 " pdb=" C4' G C 41 " pdb=" O3' G C 41 " pdb=" C2' G C 41 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CB VAL B 80 " pdb=" CA VAL B 80 " pdb=" CG1 VAL B 80 " pdb=" CG2 VAL B 80 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 3736 not shown) Planarity restraints: 3950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H 75 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO H 76 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 273 " 0.012 2.00e-02 2.50e+03 1.80e-02 5.69e+00 pdb=" CG PHE F 273 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE F 273 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 273 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE F 273 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 273 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 273 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 288 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO I 289 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO I 289 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 289 " 0.028 5.00e-02 4.00e+02 ... (remaining 3947 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3923 2.76 - 3.29: 21305 3.29 - 3.83: 39441 3.83 - 4.36: 46178 4.36 - 4.90: 81021 Nonbonded interactions: 191868 Sorted by model distance: nonbonded pdb=" O2' G C 5 " pdb=" O PHE I 21 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR B 108 " pdb=" O GLY B 124 " model vdw 2.226 3.040 nonbonded pdb=" O ALA D 143 " pdb=" OG SER D 174 " model vdw 2.226 3.040 nonbonded pdb=" O2' C C 29 " pdb=" O PHE E 21 " model vdw 2.237 3.040 nonbonded pdb=" O SER D 105 " pdb=" OG SER D 105 " model vdw 2.261 3.040 ... (remaining 191863 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 'D' and resid 12 through 332) selection = (chain 'E' and (resid 12 through 51 or resid 79 through 332)) selection = (chain 'F' and (resid 12 through 51 or resid 79 through 332)) selection = (chain 'G' and (resid 12 through 51 or resid 79 through 332)) selection = (chain 'H' and (resid 12 through 51 or resid 79 through 332)) selection = (chain 'I' and (resid 12 through 51 or resid 79 through 332)) } 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 25.120 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24609 Z= 0.218 Angle : 0.618 10.526 33700 Z= 0.409 Chirality : 0.044 0.197 3739 Planarity : 0.004 0.067 3950 Dihedral : 19.622 165.872 9784 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.42 % Allowed : 29.07 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.16), residues: 2662 helix: 0.47 (0.18), residues: 770 sheet: 1.02 (0.27), residues: 430 loop : -1.70 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 51 TYR 0.016 0.001 TYR A 142 PHE 0.041 0.001 PHE F 273 TRP 0.008 0.001 TRP J 74 HIS 0.015 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.22 (24609) covalent geometry : angle 0.61787 / 0.41 (33700) hydrogen bonds : bond 0.17420 / 11.50 ( 867) hydrogen bonds : angle 5.99629 / 4.15 ( 2446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 229 MET cc_start: 0.8355 (tpp) cc_final: 0.7945 (tpp) outliers start: 10 outliers final: 2 residues processed: 214 average time/residue: 0.1691 time to fit residues: 57.9646 Evaluate side-chains 140 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 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 = 0.3117 r_free = 0.3117 target = 0.048413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.033328 restraints weight = 116825.751| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 4.23 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24609 Z= 0.179 Angle : 0.565 7.663 33700 Z= 0.311 Chirality : 0.040 0.221 3739 Planarity : 0.004 0.060 3950 Dihedral : 16.135 163.684 4301 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.09 % Allowed : 26.81 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2662 helix: 1.22 (0.19), residues: 786 sheet: 0.93 (0.27), residues: 434 loop : -1.51 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 146 TYR 0.011 0.001 TYR A 101 PHE 0.016 0.001 PHE H 329 TRP 0.009 0.001 TRP D 149 HIS 0.006 0.001 HIS J 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (24609) covalent geometry : angle 0.56499 / 0.31 (33700) hydrogen bonds : bond 0.04780 / 3.10 ( 867) hydrogen bonds : angle 4.80260 / 3.37 ( 2446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9345 (mm) REVERT: B 71 LEU cc_start: 0.9294 (mt) cc_final: 0.9058 (mt) REVERT: B 83 TYR cc_start: 0.9107 (m-80) cc_final: 0.8809 (m-80) REVERT: B 115 MET cc_start: 0.9184 (tpt) cc_final: 0.8625 (tpt) REVERT: B 137 GLN cc_start: 0.8928 (mp10) cc_final: 0.8625 (mp10) REVERT: H 204 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8848 (ttm110) REVERT: H 229 MET cc_start: 0.9074 (tpp) cc_final: 0.7643 (tpp) REVERT: H 278 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: F 62 MET cc_start: 0.7111 (pmm) cc_final: 0.6452 (pmm) REVERT: F 120 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8470 (tm-30) REVERT: E 313 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8794 (tp) REVERT: D 221 MET cc_start: 0.7650 (mmm) cc_final: 0.7404 (mmm) REVERT: J 62 MET cc_start: 0.8051 (mpt) cc_final: 0.7824 (mmt) REVERT: J 138 MET cc_start: 0.8208 (ppp) cc_final: 0.7493 (ppp) REVERT: J 240 ASP cc_start: 0.9060 (m-30) cc_final: 0.8770 (p0) outliers start: 50 outliers final: 18 residues processed: 187 average time/residue: 0.1700 time to fit residues: 50.6639 Evaluate side-chains 147 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 272 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 141 optimal weight: 0.0010 chunk 229 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 150 optimal weight: 40.0000 chunk 86 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 overall best weight: 4.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 HIS ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN J 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.031706 restraints weight = 117845.304| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 4.22 r_work: 0.2400 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 24609 Z= 0.231 Angle : 0.575 8.292 33700 Z= 0.312 Chirality : 0.041 0.205 3739 Planarity : 0.004 0.055 3950 Dihedral : 16.219 165.544 4299 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.09 % Allowed : 26.35 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.17), residues: 2662 helix: 1.38 (0.19), residues: 792 sheet: 0.70 (0.27), residues: 429 loop : -1.47 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.013 0.001 TYR A 101 PHE 0.023 0.002 PHE H 329 TRP 0.007 0.001 TRP G 33 HIS 0.006 0.001 HIS J 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (24609) covalent geometry : angle 0.57476 / 0.31 (33700) hydrogen bonds : bond 0.04462 / 2.89 ( 867) hydrogen bonds : angle 4.61822 / 3.24 ( 2446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 122 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8186 (mmm160) cc_final: 0.7768 (mmm160) REVERT: A 146 ARG cc_start: 0.9316 (ptp-110) cc_final: 0.9088 (mtm110) REVERT: A 249 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9320 (mm) REVERT: B 83 TYR cc_start: 0.9146 (m-80) cc_final: 0.8825 (m-80) REVERT: B 115 MET cc_start: 0.9082 (tpt) cc_final: 0.8571 (tpt) REVERT: I 106 MET cc_start: 0.9303 (ttp) cc_final: 0.8966 (tmm) REVERT: H 91 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9100 (tp) REVERT: H 204 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8897 (ttm110) REVERT: H 229 MET cc_start: 0.9381 (tpp) cc_final: 0.7948 (tpp) REVERT: G 120 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8701 (tm-30) REVERT: G 304 MET cc_start: 0.9493 (ttt) cc_final: 0.9236 (tmm) REVERT: F 62 MET cc_start: 0.7191 (pmm) cc_final: 0.6768 (pmm) REVERT: E 229 MET cc_start: 0.9316 (mmp) cc_final: 0.9107 (mmp) REVERT: E 313 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8804 (tp) REVERT: D 221 MET cc_start: 0.8122 (mmm) cc_final: 0.7771 (mmm) REVERT: J 62 MET cc_start: 0.8284 (mpt) cc_final: 0.8025 (mmt) REVERT: J 138 MET cc_start: 0.8504 (ppp) cc_final: 0.8142 (ppp) REVERT: J 240 ASP cc_start: 0.9271 (m-30) cc_final: 0.8950 (p0) outliers start: 74 outliers final: 42 residues processed: 186 average time/residue: 0.1694 time to fit residues: 50.9751 Evaluate side-chains 162 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 196 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 HIS H 120 GLN ** G 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.046567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.031523 restraints weight = 117849.267| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 4.21 r_work: 0.2398 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24609 Z= 0.201 Angle : 0.544 7.484 33700 Z= 0.296 Chirality : 0.040 0.192 3739 Planarity : 0.004 0.052 3950 Dihedral : 16.243 165.797 4299 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.55 % Allowed : 26.01 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2662 helix: 1.48 (0.19), residues: 792 sheet: 0.70 (0.27), residues: 419 loop : -1.49 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 88 TYR 0.011 0.001 TYR F 210 PHE 0.020 0.001 PHE J 92 TRP 0.007 0.001 TRP G 33 HIS 0.007 0.001 HIS J 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (24609) covalent geometry : angle 0.54381 / 0.30 (33700) hydrogen bonds : bond 0.04028 / 2.61 ( 867) hydrogen bonds : angle 4.50105 / 3.15 ( 2446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 120 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8522 (tt) REVERT: A 249 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9330 (mm) REVERT: B 83 TYR cc_start: 0.9145 (m-80) cc_final: 0.8829 (m-80) REVERT: B 115 MET cc_start: 0.9085 (tpt) cc_final: 0.8600 (tpt) REVERT: B 134 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9079 (mttt) REVERT: I 106 MET cc_start: 0.9296 (ttp) cc_final: 0.8766 (tmm) REVERT: I 238 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8716 (ttmt) REVERT: H 91 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8947 (tp) REVERT: H 229 MET cc_start: 0.9363 (tpp) cc_final: 0.7866 (tpp) REVERT: G 120 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8679 (tm-30) REVERT: G 236 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9068 (mmtt) REVERT: G 304 MET cc_start: 0.9500 (ttt) cc_final: 0.9245 (tmm) REVERT: F 62 MET cc_start: 0.7263 (pmm) cc_final: 0.7051 (pmm) REVERT: F 120 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8903 (tm-30) REVERT: E 62 MET cc_start: 0.7015 (tpp) cc_final: 0.6785 (tpp) REVERT: E 106 MET cc_start: 0.8874 (ttp) cc_final: 0.8476 (tmm) REVERT: E 229 MET cc_start: 0.9186 (mmp) cc_final: 0.8834 (mmp) REVERT: E 313 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8790 (tp) REVERT: D 221 MET cc_start: 0.8240 (mmm) cc_final: 0.7999 (mmm) REVERT: D 259 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7497 (ttp80) REVERT: D 301 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9260 (tp) REVERT: J 62 MET cc_start: 0.8289 (mpt) cc_final: 0.8020 (mmt) REVERT: J 135 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8233 (tmm) REVERT: J 322 MET cc_start: 0.8184 (mmm) cc_final: 0.7936 (tpp) outliers start: 85 outliers final: 51 residues processed: 193 average time/residue: 0.1689 time to fit residues: 52.2813 Evaluate side-chains 175 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 114 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 156 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 161 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 86 optimal weight: 0.2980 chunk 261 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 HIS H 120 GLN ** G 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.046732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.031795 restraints weight = 116661.607| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 4.18 r_work: 0.2408 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24609 Z= 0.158 Angle : 0.521 8.509 33700 Z= 0.283 Chirality : 0.039 0.177 3739 Planarity : 0.004 0.051 3950 Dihedral : 16.235 165.921 4299 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.47 % Allowed : 25.89 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2662 helix: 1.54 (0.19), residues: 792 sheet: 0.73 (0.27), residues: 417 loop : -1.45 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 146 TYR 0.010 0.001 TYR B 155 PHE 0.022 0.001 PHE J 92 TRP 0.006 0.001 TRP G 33 HIS 0.007 0.001 HIS J 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (24609) covalent geometry : angle 0.52063 / 0.28 (33700) hydrogen bonds : bond 0.03808 / 2.48 ( 867) hydrogen bonds : angle 4.36487 / 3.05 ( 2446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 123 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9145 (tptp) REVERT: A 249 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9319 (mm) REVERT: B 83 TYR cc_start: 0.9135 (m-80) cc_final: 0.8810 (m-80) REVERT: B 115 MET cc_start: 0.9070 (tpt) cc_final: 0.8598 (tpt) REVERT: B 134 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9078 (mttt) REVERT: I 70 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8833 (mp0) REVERT: I 106 MET cc_start: 0.9309 (ttp) cc_final: 0.8787 (tmm) REVERT: I 238 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8768 (ttmt) REVERT: H 91 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9094 (tp) REVERT: H 229 MET cc_start: 0.9369 (tpp) cc_final: 0.7896 (tpp) REVERT: G 120 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8648 (tm-30) REVERT: G 236 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9068 (mmtt) REVERT: G 304 MET cc_start: 0.9493 (ttt) cc_final: 0.9241 (tmm) REVERT: F 120 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8866 (tm-30) REVERT: F 253 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9039 (tppt) REVERT: E 106 MET cc_start: 0.8869 (ttp) cc_final: 0.8476 (tmm) REVERT: E 221 MET cc_start: 0.9099 (mmt) cc_final: 0.8819 (mmt) REVERT: E 229 MET cc_start: 0.9129 (mmt) cc_final: 0.8904 (mmp) REVERT: E 313 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8809 (tp) REVERT: D 221 MET cc_start: 0.8228 (mmm) cc_final: 0.7979 (mmm) REVERT: D 259 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7490 (ttp80) REVERT: J 62 MET cc_start: 0.8289 (mpt) cc_final: 0.8017 (mmt) REVERT: J 135 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8186 (tmm) REVERT: J 138 MET cc_start: 0.8220 (ppp) cc_final: 0.7739 (ppp) REVERT: J 322 MET cc_start: 0.8269 (mmm) cc_final: 0.7990 (tpp) outliers start: 83 outliers final: 52 residues processed: 197 average time/residue: 0.1705 time to fit residues: 54.0308 Evaluate side-chains 182 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 119 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 271 optimal weight: 50.0000 chunk 186 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 120 GLN H 178 ASN ** G 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.046408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.031659 restraints weight = 120113.998| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 4.15 r_work: 0.2390 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24609 Z= 0.215 Angle : 0.552 8.719 33700 Z= 0.297 Chirality : 0.040 0.146 3739 Planarity : 0.004 0.051 3950 Dihedral : 16.259 167.191 4299 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.18 % Allowed : 25.14 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2662 helix: 1.46 (0.19), residues: 798 sheet: 0.59 (0.27), residues: 434 loop : -1.45 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 146 TYR 0.011 0.001 TYR F 210 PHE 0.024 0.001 PHE J 92 TRP 0.008 0.001 TRP G 33 HIS 0.006 0.001 HIS J 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (24609) covalent geometry : angle 0.55154 / 0.30 (33700) hydrogen bonds : bond 0.03887 / 2.52 ( 867) hydrogen bonds : angle 4.40291 / 3.07 ( 2446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 119 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 MET cc_start: 0.6891 (pmm) cc_final: 0.6638 (pmm) REVERT: A 51 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.7847 (mmm160) REVERT: A 73 GLN cc_start: 0.9267 (pm20) cc_final: 0.8735 (pm20) REVERT: A 249 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9335 (mm) REVERT: B 115 MET cc_start: 0.9103 (tpt) cc_final: 0.8610 (tpt) REVERT: I 70 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8888 (mp0) REVERT: I 106 MET cc_start: 0.9282 (ttp) cc_final: 0.8776 (tmm) REVERT: I 238 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8736 (ttmt) REVERT: H 91 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8948 (tp) REVERT: H 229 MET cc_start: 0.9404 (tpp) cc_final: 0.7941 (tpp) REVERT: G 120 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8662 (tm-30) REVERT: G 236 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9090 (mmtt) REVERT: F 62 MET cc_start: 0.7361 (pmm) cc_final: 0.6843 (pmm) REVERT: F 120 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8898 (tm-30) REVERT: E 106 MET cc_start: 0.8877 (ttp) cc_final: 0.8519 (tmm) REVERT: E 229 MET cc_start: 0.9080 (mmt) cc_final: 0.8810 (mmp) REVERT: E 313 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8808 (tp) REVERT: D 221 MET cc_start: 0.8251 (mmm) cc_final: 0.8005 (mmm) REVERT: D 259 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7473 (ttp80) REVERT: D 300 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9203 (mm) REVERT: D 301 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9262 (tp) REVERT: J 62 MET cc_start: 0.8260 (mpt) cc_final: 0.7995 (mmt) REVERT: J 135 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8164 (tmm) REVERT: J 138 MET cc_start: 0.8349 (ppp) cc_final: 0.7759 (ppp) REVERT: J 322 MET cc_start: 0.8355 (mmm) cc_final: 0.8020 (tpp) outliers start: 100 outliers final: 61 residues processed: 205 average time/residue: 0.1640 time to fit residues: 54.2347 Evaluate side-chains 183 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 112 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 72 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 120 GLN ** G 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN J 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.031352 restraints weight = 120357.771| |-----------------------------------------------------------------------------| r_work (start): 0.2536 rms_B_bonded: 4.14 r_work: 0.2381 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24609 Z= 0.231 Angle : 0.567 9.258 33700 Z= 0.305 Chirality : 0.040 0.152 3739 Planarity : 0.004 0.051 3950 Dihedral : 16.293 167.595 4299 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.93 % Allowed : 25.30 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2662 helix: 1.41 (0.19), residues: 799 sheet: 0.35 (0.27), residues: 437 loop : -1.43 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 71 TYR 0.012 0.001 TYR F 210 PHE 0.025 0.001 PHE J 92 TRP 0.008 0.001 TRP G 33 HIS 0.006 0.001 HIS J 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (24609) covalent geometry : angle 0.56729 / 0.31 (33700) hydrogen bonds : bond 0.03926 / 2.55 ( 867) hydrogen bonds : angle 4.44512 / 3.11 ( 2446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 112 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.7987 (mmm160) REVERT: A 163 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8379 (mmt90) REVERT: A 249 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9340 (mm) REVERT: B 115 MET cc_start: 0.9079 (tpt) cc_final: 0.8593 (tpt) REVERT: B 134 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9075 (mttt) REVERT: I 70 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8900 (mp0) REVERT: I 106 MET cc_start: 0.9266 (ttp) cc_final: 0.9023 (tmm) REVERT: I 238 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8729 (ttmt) REVERT: I 304 MET cc_start: 0.9665 (ttm) cc_final: 0.9220 (tmm) REVERT: H 91 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8933 (tp) REVERT: H 204 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8931 (ttm110) REVERT: H 229 MET cc_start: 0.9405 (tpp) cc_final: 0.7949 (tpp) REVERT: G 120 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8664 (tm-30) REVERT: G 236 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9104 (mmtt) REVERT: F 62 MET cc_start: 0.7431 (pmm) cc_final: 0.6752 (pmm) REVERT: F 120 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8924 (tm-30) REVERT: E 106 MET cc_start: 0.8880 (ttp) cc_final: 0.8525 (tmm) REVERT: E 229 MET cc_start: 0.9077 (mmt) cc_final: 0.8814 (mmp) REVERT: E 313 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8830 (tp) REVERT: D 106 MET cc_start: 0.8499 (tmm) cc_final: 0.8227 (tmm) REVERT: D 221 MET cc_start: 0.8255 (mmm) cc_final: 0.7993 (mmm) REVERT: D 229 MET cc_start: 0.7511 (ttt) cc_final: 0.7132 (ttp) REVERT: D 259 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7452 (ttp80) REVERT: D 300 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9204 (mm) REVERT: D 301 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9278 (tp) REVERT: J 62 MET cc_start: 0.8267 (mpt) cc_final: 0.8002 (mmt) REVERT: J 135 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8095 (tmm) REVERT: J 138 MET cc_start: 0.8403 (ppp) cc_final: 0.7892 (ppp) REVERT: J 322 MET cc_start: 0.8415 (mmm) cc_final: 0.8034 (tpp) outliers start: 94 outliers final: 67 residues processed: 197 average time/residue: 0.1606 time to fit residues: 51.1700 Evaluate side-chains 189 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 110 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 258 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 100 optimal weight: 0.0070 chunk 216 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 120 GLN G 333 GLN F 140 ASN ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.046833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.032068 restraints weight = 118410.779| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 4.16 r_work: 0.2407 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24609 Z= 0.128 Angle : 0.526 9.791 33700 Z= 0.282 Chirality : 0.039 0.177 3739 Planarity : 0.004 0.054 3950 Dihedral : 16.282 166.698 4299 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.93 % Allowed : 26.39 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2662 helix: 1.51 (0.19), residues: 798 sheet: 0.54 (0.27), residues: 439 loop : -1.40 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 259 TYR 0.010 0.001 TYR B 155 PHE 0.022 0.001 PHE J 92 TRP 0.007 0.001 TRP G 264 HIS 0.006 0.001 HIS J 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (24609) covalent geometry : angle 0.52649 / 0.28 (33700) hydrogen bonds : bond 0.03585 / 2.34 ( 867) hydrogen bonds : angle 4.28773 / 2.99 ( 2446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 119 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7940 (mmm160) REVERT: A 146 ARG cc_start: 0.9431 (ptp-110) cc_final: 0.9229 (mtm110) REVERT: A 163 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.8314 (mmt90) REVERT: A 249 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9327 (mm) REVERT: B 83 TYR cc_start: 0.9122 (m-80) cc_final: 0.8798 (m-80) REVERT: B 115 MET cc_start: 0.9075 (tpt) cc_final: 0.8597 (tpt) REVERT: B 134 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9053 (mttt) REVERT: B 137 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8734 (mm-40) REVERT: I 70 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8848 (mp0) REVERT: I 304 MET cc_start: 0.9666 (ttm) cc_final: 0.9225 (tmm) REVERT: H 91 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8948 (tp) REVERT: H 229 MET cc_start: 0.9361 (tpp) cc_final: 0.7877 (tpp) REVERT: G 120 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8634 (tm-30) REVERT: G 236 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9107 (mmtt) REVERT: G 333 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6870 (mm-40) REVERT: F 62 MET cc_start: 0.7399 (pmm) cc_final: 0.6625 (pmm) REVERT: F 120 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8907 (tm-30) REVERT: E 106 MET cc_start: 0.8874 (ttp) cc_final: 0.8548 (tmm) REVERT: E 221 MET cc_start: 0.9108 (mmt) cc_final: 0.8867 (mmt) REVERT: E 229 MET cc_start: 0.9023 (mmt) cc_final: 0.8770 (mmp) REVERT: E 333 GLN cc_start: 0.8866 (mm110) cc_final: 0.8619 (mm-40) REVERT: D 106 MET cc_start: 0.8515 (tmm) cc_final: 0.8250 (tmm) REVERT: D 221 MET cc_start: 0.8242 (mmm) cc_final: 0.7957 (mmm) REVERT: D 259 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7486 (ttp80) REVERT: J 62 MET cc_start: 0.8240 (mpt) cc_final: 0.7996 (mmt) REVERT: J 135 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8133 (tmm) REVERT: J 138 MET cc_start: 0.8327 (ppp) cc_final: 0.7803 (ppp) REVERT: J 233 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9291 (pp) REVERT: J 265 ARG cc_start: 0.9527 (OUTLIER) cc_final: 0.9307 (ptm-80) REVERT: J 322 MET cc_start: 0.8429 (mmm) cc_final: 0.8028 (tpp) outliers start: 70 outliers final: 52 residues processed: 180 average time/residue: 0.1675 time to fit residues: 48.0277 Evaluate side-chains 177 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 115 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 333 GLN Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 265 ARG Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 69 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 169 optimal weight: 0.6980 chunk 193 optimal weight: 9.9990 chunk 141 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 4 GLN H 120 GLN G 333 GLN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.047138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.032364 restraints weight = 117989.091| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 4.19 r_work: 0.2419 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24609 Z= 0.112 Angle : 0.528 10.645 33700 Z= 0.281 Chirality : 0.039 0.214 3739 Planarity : 0.004 0.056 3950 Dihedral : 16.264 166.790 4299 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.63 % Allowed : 26.73 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2662 helix: 1.54 (0.19), residues: 798 sheet: 0.56 (0.27), residues: 443 loop : -1.36 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 71 TYR 0.011 0.001 TYR B 155 PHE 0.025 0.001 PHE J 92 TRP 0.006 0.001 TRP H 264 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (24609) covalent geometry : angle 0.52829 / 0.28 (33700) hydrogen bonds : bond 0.03486 / 2.28 ( 867) hydrogen bonds : angle 4.19847 / 2.93 ( 2446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.7980 (mmm160) REVERT: A 146 ARG cc_start: 0.9432 (ptp-110) cc_final: 0.9231 (mtm110) REVERT: A 249 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9331 (mm) REVERT: B 83 TYR cc_start: 0.9116 (m-80) cc_final: 0.8796 (m-80) REVERT: B 115 MET cc_start: 0.9068 (tpt) cc_final: 0.8596 (tpt) REVERT: B 134 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9084 (mttt) REVERT: B 137 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8718 (mm-40) REVERT: I 70 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8834 (mp0) REVERT: I 106 MET cc_start: 0.9186 (ttp) cc_final: 0.8943 (tmm) REVERT: I 304 MET cc_start: 0.9664 (ttm) cc_final: 0.9213 (tmm) REVERT: H 91 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9084 (tp) REVERT: H 229 MET cc_start: 0.9374 (tpp) cc_final: 0.7887 (tpp) REVERT: G 120 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8627 (tm-30) REVERT: G 236 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9109 (mmtt) REVERT: G 333 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6811 (mm-40) REVERT: F 62 MET cc_start: 0.7408 (pmm) cc_final: 0.6605 (pmm) REVERT: F 120 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8914 (tm-30) REVERT: E 106 MET cc_start: 0.8870 (ttp) cc_final: 0.8539 (tmm) REVERT: E 221 MET cc_start: 0.9091 (mmt) cc_final: 0.8845 (mmt) REVERT: E 229 MET cc_start: 0.8982 (mmt) cc_final: 0.8716 (mmp) REVERT: E 333 GLN cc_start: 0.8851 (mm110) cc_final: 0.8605 (mm-40) REVERT: D 106 MET cc_start: 0.8526 (tmm) cc_final: 0.8230 (tmm) REVERT: D 221 MET cc_start: 0.8229 (mmm) cc_final: 0.7940 (mmm) REVERT: D 259 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7531 (ttp80) REVERT: J 62 MET cc_start: 0.8319 (mpt) cc_final: 0.8061 (mmt) REVERT: J 135 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8171 (tmm) REVERT: J 138 MET cc_start: 0.8271 (ppp) cc_final: 0.7852 (ppp) REVERT: J 233 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9317 (pp) REVERT: J 265 ARG cc_start: 0.9524 (OUTLIER) cc_final: 0.9301 (ptm-80) REVERT: J 322 MET cc_start: 0.8453 (mmm) cc_final: 0.8034 (tpp) outliers start: 63 outliers final: 51 residues processed: 176 average time/residue: 0.1733 time to fit residues: 48.8671 Evaluate side-chains 181 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 333 GLN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 265 ARG Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 213 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 333 GLN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.046821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.032092 restraints weight = 119622.171| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 4.16 r_work: 0.2408 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24609 Z= 0.155 Angle : 0.545 11.262 33700 Z= 0.288 Chirality : 0.040 0.325 3739 Planarity : 0.004 0.055 3950 Dihedral : 16.256 167.612 4299 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.89 % Allowed : 26.31 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.17), residues: 2662 helix: 1.56 (0.19), residues: 798 sheet: 0.44 (0.26), residues: 451 loop : -1.36 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 71 TYR 0.042 0.001 TYR A 62 PHE 0.024 0.001 PHE J 92 TRP 0.007 0.001 TRP J 74 HIS 0.002 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (24609) covalent geometry : angle 0.54488 / 0.29 (33700) hydrogen bonds : bond 0.03530 / 2.30 ( 867) hydrogen bonds : angle 4.23124 / 2.95 ( 2446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 119 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.7964 (mmm160) REVERT: A 146 ARG cc_start: 0.9438 (ptp-110) cc_final: 0.9237 (mtm110) REVERT: A 163 ARG cc_start: 0.8786 (mmm-85) cc_final: 0.8292 (mmt90) REVERT: A 249 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9331 (mm) REVERT: B 83 TYR cc_start: 0.9127 (m-80) cc_final: 0.8796 (m-80) REVERT: B 115 MET cc_start: 0.9067 (tpt) cc_final: 0.8565 (tpt) REVERT: B 134 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9086 (mttt) REVERT: B 137 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8743 (mm-40) REVERT: I 70 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8839 (mp0) REVERT: I 106 MET cc_start: 0.9205 (ttp) cc_final: 0.8944 (tmm) REVERT: I 304 MET cc_start: 0.9664 (ttm) cc_final: 0.9216 (tmm) REVERT: H 91 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8917 (tp) REVERT: H 229 MET cc_start: 0.9387 (tpp) cc_final: 0.7871 (tpp) REVERT: G 36 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8194 (p0) REVERT: G 120 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8644 (tm-30) REVERT: G 236 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9109 (mmtt) REVERT: G 304 MET cc_start: 0.9443 (ttt) cc_final: 0.9200 (tmm) REVERT: G 333 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6713 (mm-40) REVERT: F 62 MET cc_start: 0.7397 (pmm) cc_final: 0.6586 (pmm) REVERT: F 120 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8923 (tm-30) REVERT: E 106 MET cc_start: 0.8884 (ttp) cc_final: 0.8532 (tmm) REVERT: E 229 MET cc_start: 0.8975 (mmt) cc_final: 0.8709 (mmp) REVERT: E 333 GLN cc_start: 0.8866 (mm110) cc_final: 0.8620 (mm-40) REVERT: D 106 MET cc_start: 0.8537 (tmm) cc_final: 0.8271 (tmm) REVERT: D 221 MET cc_start: 0.8243 (mmm) cc_final: 0.7967 (mmm) REVERT: D 259 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7451 (ttp80) REVERT: D 301 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9253 (tp) REVERT: J 62 MET cc_start: 0.8266 (mpt) cc_final: 0.8015 (mmt) REVERT: J 135 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8121 (tmm) REVERT: J 138 MET cc_start: 0.8313 (ppp) cc_final: 0.7895 (ppp) REVERT: J 233 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9320 (pp) REVERT: J 265 ARG cc_start: 0.9530 (OUTLIER) cc_final: 0.9310 (ptm-80) REVERT: J 322 MET cc_start: 0.8500 (mmm) cc_final: 0.8079 (tpp) outliers start: 69 outliers final: 55 residues processed: 177 average time/residue: 0.1571 time to fit residues: 44.8076 Evaluate side-chains 184 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 117 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 333 GLN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 116 HIS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 250 LEU Chi-restraints excluded: chain J residue 265 ARG Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 292 TYR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 320 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 203 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 274 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 GLN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.031472 restraints weight = 120277.224| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 4.13 r_work: 0.2388 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24609 Z= 0.227 Angle : 0.581 10.962 33700 Z= 0.307 Chirality : 0.040 0.223 3739 Planarity : 0.004 0.054 3950 Dihedral : 16.278 168.640 4299 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.05 % Allowed : 26.01 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2662 helix: 1.51 (0.19), residues: 798 sheet: 0.30 (0.27), residues: 445 loop : -1.38 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 71 TYR 0.027 0.001 TYR A 62 PHE 0.024 0.001 PHE J 92 TRP 0.009 0.001 TRP G 33 HIS 0.003 0.001 HIS G 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (24609) covalent geometry : angle 0.58065 / 0.31 (33700) hydrogen bonds : bond 0.03767 / 2.45 ( 867) hydrogen bonds : angle 4.34232 / 3.03 ( 2446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5844.06 seconds wall clock time: 101 minutes 14.77 seconds (6074.77 seconds total)