Starting phenix.real_space_refine on Thu Feb 5 01:13:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l6w_62865/02_2026/9l6w_62865.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l6w_62865/02_2026/9l6w_62865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l6w_62865/02_2026/9l6w_62865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l6w_62865/02_2026/9l6w_62865.map" model { file = "/net/cci-nas-00/data/ceres_data/9l6w_62865/02_2026/9l6w_62865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l6w_62865/02_2026/9l6w_62865.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 71 5.16 5 C 8892 2.51 5 N 2385 2.21 5 O 2707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14079 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2317 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "F" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2228 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain breaks: 1 Chain: "E" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2310 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Chain: "D" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2325 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 Chain: "C" Number of atoms: 2336 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 294, 2325 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 294, 2325 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 bond proxies already assigned to first conformer: 2350 Chain: "A" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2311 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG C 74 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 74 " occ=0.50 Time building chain proxies: 3.61, per 1000 atoms: 0.26 Number of scatterers: 14079 At special positions: 0 Unit cell: (94.71, 137.35, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 18 15.00 Mg 6 11.99 O 2707 8.00 N 2385 7.00 C 8892 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: 0.93 Conformation dependent library (CDL) restraints added in 454.7 milliseconds 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 6 sheets defined 61.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.525A pdb=" N ALA B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.658A pdb=" N GLU B 85 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.717A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.569A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 206 through 222 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 removed outlier: 4.033A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 340 through 348 removed outlier: 4.369A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 61 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.524A pdb=" N ALA F 65 " --> pdb=" O PRO F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 82 through 86 removed outlier: 3.696A pdb=" N GLU F 85 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 113 through 118 removed outlier: 3.720A pdb=" N TYR F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.568A pdb=" N ILE F 162 " --> pdb=" O ARG F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.420A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 222 Processing helix chain 'F' and resid 242 through 248 Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 282 through 290 removed outlier: 4.063A pdb=" N ILE F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 340 through 348 removed outlier: 4.377A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 61 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.523A pdb=" N ALA E 65 " --> pdb=" O PRO E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.687A pdb=" N GLU E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 158 through 163 removed outlier: 3.568A pdb=" N ILE E 162 " --> pdb=" O ARG E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 206 through 222 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 removed outlier: 4.169A pdb=" N ILE E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 310 through 320 Processing helix chain 'E' and resid 340 through 348 removed outlier: 4.378A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.604A pdb=" N ALA D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.660A pdb=" N GLU D 85 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.717A pdb=" N TYR D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.568A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 206 through 222 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 4.209A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 340 through 348 removed outlier: 4.381A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.523A pdb=" N ALA C 65 " --> pdb=" O PRO C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.681A pdb=" N GLU C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.568A pdb=" N ILE C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 206 through 222 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 removed outlier: 4.105A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 340 through 348 removed outlier: 4.382A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 61 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.576A pdb=" N ALA A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.694A pdb=" N GLU A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.569A pdb=" N ILE A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.167A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.545A pdb=" N ASP A 240 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.941A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 340 through 348 removed outlier: 4.363A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 153 through 157 removed outlier: 6.160A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 191 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 234 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 153 through 157 removed outlier: 6.160A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 191 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA F 234 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL F 129 " --> pdb=" O GLY F 233 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR F 235 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU F 131 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 153 through 157 removed outlier: 6.161A pdb=" N ASN E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N PHE E 190 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE E 191 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.972A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE D 190 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 191 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 153 through 157 removed outlier: 6.161A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 191 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL C 129 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR C 235 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU C 131 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 153 through 157 removed outlier: 6.161A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 191 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 234 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3003 1.33 - 1.45: 2841 1.45 - 1.57: 8308 1.57 - 1.69: 31 1.69 - 1.81: 124 Bond restraints: 14307 Sorted by residual: bond pdb=" C4 ATP F 401 " pdb=" C5 ATP F 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.60e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C4 ATP E 401 " pdb=" C5 ATP E 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.49e+01 bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.41e+01 bond pdb=" C4 ATP D 401 " pdb=" C5 ATP D 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.40e+01 ... (remaining 14302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 18832 3.63 - 7.26: 411 7.26 - 10.89: 62 10.89 - 14.52: 11 14.52 - 18.14: 11 Bond angle restraints: 19327 Sorted by residual: angle pdb=" PB ATP D 401 " pdb=" O3B ATP D 401 " pdb=" PG ATP D 401 " ideal model delta sigma weight residual 139.87 121.73 18.14 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.80 18.07 1.00e+00 1.00e+00 3.27e+02 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 121.99 17.88 1.00e+00 1.00e+00 3.20e+02 angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 122.62 17.25 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 123.33 16.54 1.00e+00 1.00e+00 2.74e+02 ... (remaining 19322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7621 17.78 - 35.56: 1049 35.56 - 53.34: 225 53.34 - 71.12: 70 71.12 - 88.89: 28 Dihedral angle restraints: 8993 sinusoidal: 3851 harmonic: 5142 Sorted by residual: dihedral pdb=" CA LEU D 249 " pdb=" C LEU D 249 " pdb=" N PRO D 250 " pdb=" CA PRO D 250 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA LEU E 249 " pdb=" C LEU E 249 " pdb=" N PRO E 250 " pdb=" CA PRO E 250 " ideal model delta harmonic sigma weight residual 180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" C THR C 140 " pdb=" N THR C 140 " pdb=" CA THR C 140 " pdb=" CB THR C 140 " ideal model delta harmonic sigma weight residual -122.00 -135.65 13.65 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 8990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1988 0.113 - 0.226: 194 0.226 - 0.338: 27 0.338 - 0.451: 2 0.451 - 0.564: 1 Chirality restraints: 2212 Sorted by residual: chirality pdb=" CA THR C 140 " pdb=" N THR C 140 " pdb=" C THR C 140 " pdb=" CB THR C 140 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.96e+00 chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA PRO F 250 " pdb=" N PRO F 250 " pdb=" C PRO F 250 " pdb=" CB PRO F 250 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 2209 not shown) Planarity restraints: 2424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 299 " -0.025 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C LYS E 299 " 0.087 2.00e-02 2.50e+03 pdb=" O LYS E 299 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU E 300 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 283 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.80e+00 pdb=" C LEU A 283 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU A 283 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN A 284 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 219 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C LEU B 219 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU B 219 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP B 220 " 0.015 2.00e-02 2.50e+03 ... (remaining 2421 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 75 2.45 - 3.07: 9081 3.07 - 3.68: 22428 3.68 - 4.29: 33752 4.29 - 4.90: 54645 Nonbonded interactions: 119981 Sorted by model distance: nonbonded pdb=" O2G ATP F 401 " pdb="MG MG F 402 " model vdw 1.844 2.170 nonbonded pdb=" O3G ATP C 401 " pdb="MG MG C 402 " model vdw 2.182 2.170 nonbonded pdb=" O LEU C 146 " pdb=" OG SER C 150 " model vdw 2.279 3.040 nonbonded pdb=" O LEU F 146 " pdb=" OG SER F 150 " model vdw 2.280 3.040 nonbonded pdb=" O LEU A 146 " pdb=" OG SER A 150 " model vdw 2.280 3.040 ... (remaining 119976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 51 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'B' and (resid 51 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'C' and (resid 51 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'D' and (resid 51 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'E' and (resid 51 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'F' and (resid 51 through 73 or resid 75 through 402)) } 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=0.00 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: 11.180 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: 0.000 Extract box with map and model: 0.820 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.750 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 14307 Z= 0.464 Angle : 1.297 18.145 19327 Z= 0.823 Chirality : 0.071 0.564 2212 Planarity : 0.007 0.054 2424 Dihedral : 17.691 88.894 5641 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.20 % Allowed : 13.33 % Favored : 84.47 % Cbeta Deviations : 0.06 % 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: -1.30 (0.20), residues: 1726 helix: -0.63 (0.16), residues: 1008 sheet: -0.86 (0.41), residues: 149 loop : -0.95 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 44 TYR 0.018 0.002 TYR E 117 PHE 0.024 0.004 PHE F 90 TRP 0.015 0.002 TRP E 220 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00685 (14307) covalent geometry : angle 1.29739 (19327) hydrogen bonds : bond 0.15357 ( 675) hydrogen bonds : angle 6.63599 ( 1981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 434 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.7549 (ptp) cc_final: 0.7320 (ptt) REVERT: B 149 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6232 (tt0) REVERT: B 315 LYS cc_start: 0.7917 (mttt) cc_final: 0.7650 (tptp) REVERT: E 53 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7615 (mm-40) REVERT: E 215 GLU cc_start: 0.7656 (tp30) cc_final: 0.7350 (mm-30) REVERT: D 80 ILE cc_start: 0.8083 (mt) cc_final: 0.7802 (mt) REVERT: D 102 ASP cc_start: 0.7848 (t0) cc_final: 0.7346 (t0) REVERT: D 124 GLN cc_start: 0.7054 (pt0) cc_final: 0.6840 (pt0) REVERT: D 243 ASP cc_start: 0.7615 (m-30) cc_final: 0.7369 (t0) REVERT: D 261 ASP cc_start: 0.7184 (m-30) cc_final: 0.6942 (p0) REVERT: A 89 THR cc_start: 0.7361 (p) cc_final: 0.6908 (m) REVERT: A 228 ARG cc_start: 0.6934 (mtm-85) cc_final: 0.6649 (ttp-110) outliers start: 33 outliers final: 2 residues processed: 451 average time/residue: 0.1348 time to fit residues: 83.7806 Evaluate side-chains 286 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 283 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN C 53 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN A 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.203202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.159685 restraints weight = 27891.597| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.42 r_work: 0.3661 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14307 Z= 0.142 Angle : 0.662 9.342 19327 Z= 0.321 Chirality : 0.044 0.206 2212 Planarity : 0.004 0.037 2424 Dihedral : 10.506 78.530 2097 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.27 % Allowed : 18.77 % Favored : 78.96 % 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: 0.22 (0.21), residues: 1726 helix: 0.82 (0.17), residues: 976 sheet: -1.04 (0.40), residues: 156 loop : -0.48 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 44 TYR 0.010 0.001 TYR B 109 PHE 0.016 0.002 PHE B 245 TRP 0.010 0.001 TRP E 220 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00341 (14307) covalent geometry : angle 0.66186 (19327) hydrogen bonds : bond 0.03842 ( 675) hydrogen bonds : angle 4.83570 ( 1981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 302 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6481 (tt0) REVERT: B 262 GLN cc_start: 0.8269 (mt0) cc_final: 0.7454 (mt0) REVERT: B 315 LYS cc_start: 0.8138 (mttt) cc_final: 0.7616 (tptp) REVERT: B 337 ARG cc_start: 0.7481 (ttp80) cc_final: 0.6585 (ttp80) REVERT: F 124 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7145 (pm20) REVERT: F 205 ASP cc_start: 0.8099 (m-30) cc_final: 0.7874 (m-30) REVERT: F 245 PHE cc_start: 0.7845 (m-80) cc_final: 0.7571 (m-80) REVERT: F 263 ARG cc_start: 0.5491 (mtm180) cc_final: 0.5219 (mtm180) REVERT: E 68 THR cc_start: 0.8094 (p) cc_final: 0.7883 (t) REVERT: E 112 MET cc_start: 0.8124 (mmm) cc_final: 0.7912 (mmm) REVERT: E 159 MET cc_start: 0.7969 (mmt) cc_final: 0.7738 (tpt) REVERT: E 215 GLU cc_start: 0.8263 (tp30) cc_final: 0.8036 (tp30) REVERT: D 80 ILE cc_start: 0.8443 (mt) cc_final: 0.8060 (mt) REVERT: D 124 GLN cc_start: 0.7530 (pt0) cc_final: 0.7219 (pt0) REVERT: D 243 ASP cc_start: 0.8335 (m-30) cc_final: 0.7906 (t0) REVERT: D 261 ASP cc_start: 0.7986 (m-30) cc_final: 0.7177 (p0) REVERT: D 348 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7898 (pp) REVERT: A 88 ILE cc_start: 0.8647 (mm) cc_final: 0.8336 (mm) REVERT: A 228 ARG cc_start: 0.6838 (mtm-85) cc_final: 0.6408 (ttp-110) REVERT: A 230 MET cc_start: 0.7320 (tpp) cc_final: 0.7033 (tpp) REVERT: A 273 ASP cc_start: 0.7862 (m-30) cc_final: 0.7112 (t0) REVERT: A 307 LEU cc_start: 0.8190 (mm) cc_final: 0.7990 (mm) REVERT: A 340 LYS cc_start: 0.8082 (pttt) cc_final: 0.7396 (pttp) REVERT: A 350 MET cc_start: 0.5607 (tpp) cc_final: 0.4835 (ptt) outliers start: 34 outliers final: 17 residues processed: 322 average time/residue: 0.1162 time to fit residues: 54.2918 Evaluate side-chains 286 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 8 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 chunk 155 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 2 optimal weight: 0.0050 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 236 ASN E 50 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN D 182 ASN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.200840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158931 restraints weight = 22975.143| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.08 r_work: 0.3653 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14307 Z= 0.123 Angle : 0.593 8.552 19327 Z= 0.283 Chirality : 0.042 0.168 2212 Planarity : 0.003 0.027 2424 Dihedral : 10.108 84.242 2093 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.85 % Allowed : 20.13 % Favored : 77.02 % 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: 0.86 (0.22), residues: 1726 helix: 1.24 (0.18), residues: 985 sheet: -0.74 (0.41), residues: 159 loop : -0.02 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 248 TYR 0.013 0.001 TYR E 264 PHE 0.014 0.002 PHE B 245 TRP 0.007 0.001 TRP E 220 HIS 0.003 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00295 (14307) covalent geometry : angle 0.59287 (19327) hydrogen bonds : bond 0.03273 ( 675) hydrogen bonds : angle 4.53670 ( 1981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 GLN cc_start: 0.8206 (mt0) cc_final: 0.7532 (mt0) REVERT: B 281 PHE cc_start: 0.7664 (t80) cc_final: 0.7357 (t80) REVERT: B 315 LYS cc_start: 0.8166 (mttt) cc_final: 0.7658 (tptp) REVERT: B 337 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7333 (ttp80) REVERT: B 350 MET cc_start: 0.6235 (mpp) cc_final: 0.5753 (mmp) REVERT: F 124 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: F 205 ASP cc_start: 0.8058 (m-30) cc_final: 0.7846 (m-30) REVERT: E 53 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7605 (mp10) REVERT: E 158 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.6720 (mtm110) REVERT: E 289 ASN cc_start: 0.8094 (m-40) cc_final: 0.7809 (t0) REVERT: D 59 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7798 (pttt) REVERT: D 261 ASP cc_start: 0.8148 (m-30) cc_final: 0.7388 (p0) REVERT: D 350 MET cc_start: 0.4913 (OUTLIER) cc_final: 0.4366 (ttt) REVERT: C 311 LYS cc_start: 0.8419 (mmtm) cc_final: 0.7606 (ptmt) REVERT: A 273 ASP cc_start: 0.7867 (m-30) cc_final: 0.7038 (t0) REVERT: A 340 LYS cc_start: 0.8068 (pttt) cc_final: 0.7563 (pttp) REVERT: A 342 LYS cc_start: 0.6953 (tttt) cc_final: 0.6353 (tptt) REVERT: A 350 MET cc_start: 0.5661 (tpp) cc_final: 0.4829 (ptt) outliers start: 43 outliers final: 20 residues processed: 296 average time/residue: 0.1170 time to fit residues: 50.3492 Evaluate side-chains 272 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.195810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150210 restraints weight = 18605.727| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.48 r_work: 0.3657 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14307 Z= 0.132 Angle : 0.587 9.828 19327 Z= 0.281 Chirality : 0.043 0.252 2212 Planarity : 0.003 0.027 2424 Dihedral : 10.188 88.259 2090 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.65 % Allowed : 20.65 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1726 helix: 1.36 (0.18), residues: 982 sheet: -0.45 (0.44), residues: 137 loop : -0.00 (0.28), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.013 0.001 TYR B 313 PHE 0.023 0.002 PHE A 245 TRP 0.007 0.001 TRP D 220 HIS 0.002 0.000 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00321 (14307) covalent geometry : angle 0.58696 (19327) hydrogen bonds : bond 0.03116 ( 675) hydrogen bonds : angle 4.50212 ( 1981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.7596 (ptp) cc_final: 0.7330 (ptt) REVERT: B 149 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6525 (tt0) REVERT: B 262 GLN cc_start: 0.8182 (mt0) cc_final: 0.7606 (mt0) REVERT: B 281 PHE cc_start: 0.7764 (t80) cc_final: 0.7459 (t80) REVERT: B 315 LYS cc_start: 0.8180 (mttt) cc_final: 0.7704 (tptp) REVERT: B 350 MET cc_start: 0.6303 (mpp) cc_final: 0.6015 (mmp) REVERT: F 124 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: E 158 ARG cc_start: 0.7328 (mtm-85) cc_final: 0.6925 (mtm110) REVERT: E 289 ASN cc_start: 0.8179 (m-40) cc_final: 0.7508 (t0) REVERT: E 350 MET cc_start: 0.6148 (mmt) cc_final: 0.4774 (mmt) REVERT: D 59 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7772 (pttt) REVERT: D 124 GLN cc_start: 0.7269 (pm20) cc_final: 0.7004 (mm-40) REVERT: D 340 LYS cc_start: 0.7187 (pttt) cc_final: 0.6811 (ptpt) REVERT: C 311 LYS cc_start: 0.8479 (mmtm) cc_final: 0.7679 (ptmt) REVERT: A 158 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7513 (mtm-85) REVERT: A 273 ASP cc_start: 0.7840 (m-30) cc_final: 0.7094 (t0) REVERT: A 340 LYS cc_start: 0.8158 (pttt) cc_final: 0.7665 (pttp) REVERT: A 342 LYS cc_start: 0.7064 (tttt) cc_final: 0.6493 (tptt) outliers start: 40 outliers final: 25 residues processed: 295 average time/residue: 0.1069 time to fit residues: 46.4419 Evaluate side-chains 279 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 274 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 86 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 134 optimal weight: 0.0970 chunk 147 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.196800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145436 restraints weight = 30159.912| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.39 r_work: 0.3565 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14307 Z= 0.130 Angle : 0.580 9.215 19327 Z= 0.276 Chirality : 0.042 0.134 2212 Planarity : 0.003 0.028 2424 Dihedral : 10.094 79.555 2090 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.91 % Allowed : 21.49 % Favored : 75.60 % 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: 1.14 (0.22), residues: 1726 helix: 1.36 (0.18), residues: 992 sheet: -0.61 (0.41), residues: 163 loop : 0.30 (0.29), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 201 TYR 0.013 0.001 TYR E 264 PHE 0.022 0.002 PHE E 344 TRP 0.007 0.001 TRP F 220 HIS 0.002 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00317 (14307) covalent geometry : angle 0.58033 (19327) hydrogen bonds : bond 0.03058 ( 675) hydrogen bonds : angle 4.48162 ( 1981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.7607 (ptp) cc_final: 0.7278 (ptt) REVERT: B 149 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: B 262 GLN cc_start: 0.8233 (mt0) cc_final: 0.7695 (mt0) REVERT: B 281 PHE cc_start: 0.7869 (t80) cc_final: 0.7601 (t80) REVERT: B 315 LYS cc_start: 0.8199 (mttt) cc_final: 0.7682 (tptp) REVERT: F 124 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: E 158 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.6917 (mtm110) REVERT: E 289 ASN cc_start: 0.8266 (m-40) cc_final: 0.7863 (t0) REVERT: D 59 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7880 (pttt) REVERT: D 340 LYS cc_start: 0.7257 (pttt) cc_final: 0.6876 (ptpt) REVERT: C 311 LYS cc_start: 0.8519 (mmtm) cc_final: 0.7642 (ptmt) REVERT: A 109 TYR cc_start: 0.6757 (m-80) cc_final: 0.6484 (m-80) REVERT: A 158 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: A 340 LYS cc_start: 0.8084 (pttt) cc_final: 0.7487 (pttp) outliers start: 43 outliers final: 25 residues processed: 297 average time/residue: 0.1089 time to fit residues: 46.9393 Evaluate side-chains 280 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 274 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 131 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 182 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** 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 = 0.4219 r_free = 0.4219 target = 0.194556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142283 restraints weight = 33550.413| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.59 r_work: 0.3522 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14307 Z= 0.143 Angle : 0.596 8.477 19327 Z= 0.283 Chirality : 0.042 0.137 2212 Planarity : 0.003 0.029 2424 Dihedral : 10.125 79.111 2090 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.59 % Allowed : 22.78 % Favored : 74.63 % 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: 1.23 (0.22), residues: 1726 helix: 1.42 (0.18), residues: 986 sheet: -0.38 (0.44), residues: 149 loop : 0.28 (0.28), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 158 TYR 0.010 0.001 TYR E 264 PHE 0.016 0.002 PHE A 253 TRP 0.009 0.001 TRP D 220 HIS 0.002 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00351 (14307) covalent geometry : angle 0.59606 (19327) hydrogen bonds : bond 0.03128 ( 675) hydrogen bonds : angle 4.54549 ( 1981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6696 (tt0) REVERT: B 175 ASP cc_start: 0.8295 (t70) cc_final: 0.8041 (t0) REVERT: B 281 PHE cc_start: 0.7968 (t80) cc_final: 0.7697 (t80) REVERT: B 315 LYS cc_start: 0.8222 (mttt) cc_final: 0.7672 (tptp) REVERT: B 337 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7351 (ttp80) REVERT: B 350 MET cc_start: 0.6610 (mmp) cc_final: 0.5535 (tpp) REVERT: F 104 HIS cc_start: 0.7532 (m-70) cc_final: 0.7292 (m-70) REVERT: F 124 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: E 158 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.6983 (mtm110) REVERT: E 289 ASN cc_start: 0.8355 (m-40) cc_final: 0.8019 (t0) REVERT: D 80 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8221 (mt) REVERT: D 159 MET cc_start: 0.7991 (mmm) cc_final: 0.7612 (mmm) REVERT: D 163 MET cc_start: 0.8318 (mtm) cc_final: 0.7817 (mtt) REVERT: D 340 LYS cc_start: 0.7407 (pttt) cc_final: 0.6932 (ptpp) REVERT: C 307 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8359 (mm) REVERT: C 311 LYS cc_start: 0.8531 (mmtm) cc_final: 0.7649 (ptmt) REVERT: C 340 LYS cc_start: 0.8117 (pttt) cc_final: 0.7901 (mttt) REVERT: A 109 TYR cc_start: 0.6730 (m-80) cc_final: 0.6449 (m-80) REVERT: A 307 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7990 (mm) REVERT: A 340 LYS cc_start: 0.8028 (pttt) cc_final: 0.7407 (pttm) REVERT: A 350 MET cc_start: 0.5572 (tpp) cc_final: 0.4192 (mtm) outliers start: 38 outliers final: 23 residues processed: 283 average time/residue: 0.1109 time to fit residues: 45.9685 Evaluate side-chains 276 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 348 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 68 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 0.0030 chunk 149 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 171 optimal weight: 0.2980 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.194993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147101 restraints weight = 23516.789| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.09 r_work: 0.3571 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14307 Z= 0.135 Angle : 0.593 10.696 19327 Z= 0.282 Chirality : 0.042 0.153 2212 Planarity : 0.003 0.029 2424 Dihedral : 10.073 78.770 2090 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.46 % Allowed : 23.75 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.22), residues: 1726 helix: 1.45 (0.18), residues: 989 sheet: -0.58 (0.43), residues: 152 loop : 0.50 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 158 TYR 0.022 0.001 TYR E 264 PHE 0.019 0.002 PHE E 344 TRP 0.007 0.001 TRP D 220 HIS 0.002 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00332 (14307) covalent geometry : angle 0.59347 (19327) hydrogen bonds : bond 0.03069 ( 675) hydrogen bonds : angle 4.48933 ( 1981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.7581 (ptp) cc_final: 0.7263 (ptt) REVERT: B 149 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: B 175 ASP cc_start: 0.8317 (t70) cc_final: 0.8104 (t0) REVERT: B 262 GLN cc_start: 0.8364 (mt0) cc_final: 0.7523 (mt0) REVERT: B 281 PHE cc_start: 0.8044 (t80) cc_final: 0.7811 (t80) REVERT: B 315 LYS cc_start: 0.8221 (mttt) cc_final: 0.7703 (tptp) REVERT: B 337 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7337 (ttp80) REVERT: B 340 LYS cc_start: 0.7731 (pttt) cc_final: 0.7374 (ptpp) REVERT: B 350 MET cc_start: 0.6636 (mmp) cc_final: 0.6220 (tpp) REVERT: F 106 SER cc_start: 0.7437 (t) cc_final: 0.7138 (m) REVERT: F 124 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: E 289 ASN cc_start: 0.8332 (m-40) cc_final: 0.8019 (t0) REVERT: D 80 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8170 (mt) REVERT: D 340 LYS cc_start: 0.7465 (pttt) cc_final: 0.6985 (ptpp) REVERT: C 49 LYS cc_start: 0.7862 (tttm) cc_final: 0.7604 (tptm) REVERT: C 54 TRP cc_start: 0.8370 (t-100) cc_final: 0.8130 (t-100) REVERT: C 307 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8374 (mm) REVERT: C 311 LYS cc_start: 0.8558 (mmtm) cc_final: 0.7677 (ptmt) REVERT: A 109 TYR cc_start: 0.6703 (m-80) cc_final: 0.6421 (m-80) REVERT: A 307 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7991 (mm) REVERT: A 350 MET cc_start: 0.5590 (tpp) cc_final: 0.4173 (mtm) outliers start: 36 outliers final: 21 residues processed: 281 average time/residue: 0.1148 time to fit residues: 47.1504 Evaluate side-chains 264 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 307 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 119 optimal weight: 0.9990 chunk 164 optimal weight: 0.1980 chunk 33 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 52 optimal weight: 0.0570 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN F 153 ASN F 193 GLN E 50 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.198470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.149496 restraints weight = 29138.659| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.33 r_work: 0.3599 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14307 Z= 0.110 Angle : 0.579 10.955 19327 Z= 0.273 Chirality : 0.042 0.161 2212 Planarity : 0.003 0.031 2424 Dihedral : 9.758 79.305 2090 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.07 % Allowed : 24.40 % Favored : 73.53 % 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: 1.42 (0.22), residues: 1726 helix: 1.45 (0.18), residues: 1002 sheet: -0.46 (0.43), residues: 152 loop : 0.65 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.020 0.001 TYR F 264 PHE 0.010 0.001 PHE F 253 TRP 0.006 0.001 TRP A 220 HIS 0.001 0.000 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00266 (14307) covalent geometry : angle 0.57917 (19327) hydrogen bonds : bond 0.02908 ( 675) hydrogen bonds : angle 4.38179 ( 1981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7276 (tmm-80) cc_final: 0.6952 (ttt-90) REVERT: B 113 MET cc_start: 0.7599 (ptp) cc_final: 0.7319 (ptt) REVERT: B 149 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6492 (tt0) REVERT: B 175 ASP cc_start: 0.8303 (t70) cc_final: 0.7962 (t0) REVERT: B 262 GLN cc_start: 0.8337 (mt0) cc_final: 0.7535 (mt0) REVERT: B 315 LYS cc_start: 0.8237 (mttt) cc_final: 0.7681 (tptp) REVERT: B 340 LYS cc_start: 0.7659 (pttt) cc_final: 0.7322 (ptpp) REVERT: B 350 MET cc_start: 0.6554 (mmp) cc_final: 0.5414 (tpp) REVERT: F 106 SER cc_start: 0.7436 (t) cc_final: 0.7139 (m) REVERT: F 124 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: E 289 ASN cc_start: 0.8387 (m-40) cc_final: 0.7853 (t0) REVERT: D 163 MET cc_start: 0.8271 (mtm) cc_final: 0.8031 (mtt) REVERT: D 340 LYS cc_start: 0.7391 (pttt) cc_final: 0.6943 (ptpp) REVERT: C 307 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8421 (mm) REVERT: C 311 LYS cc_start: 0.8566 (mmtm) cc_final: 0.7694 (ptmt) REVERT: C 337 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7403 (ttp80) REVERT: A 215 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8183 (tt0) REVERT: A 307 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8015 (mm) REVERT: A 340 LYS cc_start: 0.7905 (pttt) cc_final: 0.7377 (pttp) REVERT: A 350 MET cc_start: 0.5649 (tpp) cc_final: 0.4142 (mtm) outliers start: 30 outliers final: 17 residues processed: 277 average time/residue: 0.1115 time to fit residues: 45.5048 Evaluate side-chains 259 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 307 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 4 optimal weight: 0.0050 chunk 85 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 140 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.196458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.148937 restraints weight = 26584.425| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.53 r_work: 0.3571 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14307 Z= 0.128 Angle : 0.598 11.075 19327 Z= 0.283 Chirality : 0.042 0.175 2212 Planarity : 0.003 0.032 2424 Dihedral : 9.824 81.438 2090 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.01 % Allowed : 24.53 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.22), residues: 1726 helix: 1.54 (0.18), residues: 989 sheet: -0.51 (0.43), residues: 152 loop : 0.73 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.021 0.001 TYR B 313 PHE 0.014 0.001 PHE F 253 TRP 0.006 0.001 TRP D 220 HIS 0.002 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00315 (14307) covalent geometry : angle 0.59807 (19327) hydrogen bonds : bond 0.02937 ( 675) hydrogen bonds : angle 4.39495 ( 1981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7300 (tmm-80) cc_final: 0.7005 (ttt-90) REVERT: B 113 MET cc_start: 0.7596 (ptp) cc_final: 0.7372 (ptt) REVERT: B 149 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6547 (tt0) REVERT: B 175 ASP cc_start: 0.8301 (t70) cc_final: 0.7880 (t0) REVERT: B 262 GLN cc_start: 0.8358 (mt0) cc_final: 0.7589 (mt0) REVERT: B 315 LYS cc_start: 0.8267 (mttt) cc_final: 0.7722 (tptp) REVERT: B 337 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7398 (ttp80) REVERT: B 340 LYS cc_start: 0.7729 (pttt) cc_final: 0.7442 (ptpp) REVERT: F 104 HIS cc_start: 0.7229 (m-70) cc_final: 0.6960 (m-70) REVERT: F 124 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: F 230 MET cc_start: 0.7577 (ttt) cc_final: 0.7330 (ttt) REVERT: E 289 ASN cc_start: 0.8374 (m-40) cc_final: 0.7959 (t0) REVERT: E 344 PHE cc_start: 0.7113 (m-10) cc_final: 0.6720 (m-80) REVERT: D 80 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8129 (mt) REVERT: D 340 LYS cc_start: 0.7441 (pttt) cc_final: 0.6986 (ptpp) REVERT: C 307 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8405 (mm) REVERT: C 311 LYS cc_start: 0.8566 (mmtm) cc_final: 0.7689 (ptmt) REVERT: C 337 ARG cc_start: 0.7686 (ttm170) cc_final: 0.7428 (ttp80) REVERT: A 215 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: A 340 LYS cc_start: 0.7875 (pttt) cc_final: 0.7338 (pttp) REVERT: A 350 MET cc_start: 0.5724 (tpp) cc_final: 0.4160 (mtm) outliers start: 29 outliers final: 17 residues processed: 269 average time/residue: 0.1212 time to fit residues: 47.6759 Evaluate side-chains 266 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 236 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 62 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 91 optimal weight: 0.0050 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 0.1980 chunk 117 optimal weight: 0.0030 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** C 289 ASN ** 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 = 0.4254 r_free = 0.4254 target = 0.198000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152065 restraints weight = 20224.573| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.94 r_work: 0.3630 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14307 Z= 0.119 Angle : 0.617 16.724 19327 Z= 0.287 Chirality : 0.042 0.175 2212 Planarity : 0.003 0.032 2424 Dihedral : 9.700 83.257 2090 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.75 % Allowed : 24.98 % Favored : 73.27 % 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: 1.55 (0.22), residues: 1726 helix: 1.56 (0.18), residues: 989 sheet: -0.45 (0.43), residues: 152 loop : 0.75 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.018 0.001 TYR E 264 PHE 0.012 0.001 PHE F 253 TRP 0.007 0.001 TRP B 220 HIS 0.001 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00290 (14307) covalent geometry : angle 0.61661 (19327) hydrogen bonds : bond 0.02921 ( 675) hydrogen bonds : angle 4.38250 ( 1981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: B 113 MET cc_start: 0.7619 (ptp) cc_final: 0.7407 (ptt) REVERT: B 149 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: B 175 ASP cc_start: 0.8212 (t70) cc_final: 0.7695 (t0) REVERT: B 262 GLN cc_start: 0.8350 (mt0) cc_final: 0.7597 (mt0) REVERT: B 315 LYS cc_start: 0.8240 (mttt) cc_final: 0.7687 (tptp) REVERT: B 337 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7358 (ttp80) REVERT: B 340 LYS cc_start: 0.7825 (pttt) cc_final: 0.7530 (ptpp) REVERT: F 124 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: E 215 GLU cc_start: 0.8738 (tp30) cc_final: 0.7491 (tp30) REVERT: E 289 ASN cc_start: 0.8387 (m-40) cc_final: 0.7975 (t0) REVERT: E 344 PHE cc_start: 0.7027 (m-10) cc_final: 0.6627 (m-80) REVERT: D 80 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8059 (mt) REVERT: D 340 LYS cc_start: 0.7468 (pttt) cc_final: 0.7009 (ptpp) REVERT: C 307 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8420 (mm) REVERT: C 311 LYS cc_start: 0.8568 (mmtm) cc_final: 0.7693 (ptmt) REVERT: C 337 ARG cc_start: 0.7654 (ttm170) cc_final: 0.7403 (ttp80) REVERT: A 69 LEU cc_start: 0.6708 (tp) cc_final: 0.5830 (pp) REVERT: A 340 LYS cc_start: 0.7867 (pttt) cc_final: 0.7344 (pttp) REVERT: A 350 MET cc_start: 0.5712 (tpp) cc_final: 0.4047 (mtm) outliers start: 25 outliers final: 18 residues processed: 267 average time/residue: 0.1177 time to fit residues: 45.8651 Evaluate side-chains 264 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 236 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.0030 chunk 8 optimal weight: 0.0770 chunk 172 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.5948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.198007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.155283 restraints weight = 22392.876| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.84 r_work: 0.3622 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14307 Z= 0.120 Angle : 0.630 14.382 19327 Z= 0.294 Chirality : 0.043 0.216 2212 Planarity : 0.003 0.034 2424 Dihedral : 9.612 85.014 2090 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.88 % Allowed : 24.98 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1726 helix: 1.55 (0.18), residues: 991 sheet: -0.44 (0.45), residues: 140 loop : 0.72 (0.28), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.026 0.001 TYR B 313 PHE 0.013 0.001 PHE F 253 TRP 0.007 0.001 TRP A 220 HIS 0.001 0.000 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00290 (14307) covalent geometry : angle 0.63038 (19327) hydrogen bonds : bond 0.02927 ( 675) hydrogen bonds : angle 4.37392 ( 1981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4297.12 seconds wall clock time: 74 minutes 9.84 seconds (4449.84 seconds total)