Starting phenix.real_space_refine on Thu Feb 5 00:42:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l9h_62906/02_2026/9l9h_62906.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l9h_62906/02_2026/9l9h_62906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l9h_62906/02_2026/9l9h_62906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l9h_62906/02_2026/9l9h_62906.map" model { file = "/net/cci-nas-00/data/ceres_data/9l9h_62906/02_2026/9l9h_62906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l9h_62906/02_2026/9l9h_62906.cif" } resolution = 2.87 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= 0.012 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 8861 2.51 5 N 2371 2.21 5 O 2701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 14028 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2155 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain breaks: 1 Chain: "B" Number of atoms: 2313 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 291, 2302 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 291, 2302 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 bond proxies already assigned to first conformer: 2327 Chain: "C" 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: "D" Number of atoms: 2341 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 bond proxies already assigned to first conformer: 2361 Chain: "E" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "F" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: "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: "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: "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: "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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 74 " occ=0.46 ... (20 atoms not shown) pdb=" NH2BARG B 74 " occ=0.54 Time building chain proxies: 4.08, per 1000 atoms: 0.29 Number of scatterers: 14028 At special positions: 0 Unit cell: (91.84, 136.12, 133.66, 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 2701 8.00 N 2371 7.00 C 8861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 636.6 milliseconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 6 sheets defined 64.4% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 51 through 61 Processing helix 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 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 106 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 116 through 120 removed outlier: 4.391A pdb=" N ASN A 119 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.534A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.313A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 294 through 311 Processing helix chain 'A' and resid 340 through 348 removed outlier: 4.124A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 Processing helix 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 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 116 through 120 removed outlier: 4.390A pdb=" N ASN B 119 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 120 " --> pdb=" O TYR B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 120' Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 168 through 184 removed outlier: 3.535A pdb=" N LYS B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.295A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 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 Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 340 through 348 removed outlier: 4.126A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 61 Processing helix 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 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 116 through 120 removed outlier: 4.392A pdb=" N ASN C 119 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 120 " --> pdb=" O TYR C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 120' Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.534A pdb=" N LYS C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.295A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) 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 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: 4.126A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 Processing helix 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 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 116 through 120 removed outlier: 4.391A pdb=" N ASN D 119 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.534A pdb=" N LYS D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.318A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 340 through 348 removed outlier: 4.126A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Processing helix 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 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 116 through 120 removed outlier: 4.391A pdb=" N ASN E 119 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 184 removed outlier: 3.534A pdb=" N LYS E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.321A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) 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 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: 4.126A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 Processing helix 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 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.519A pdb=" N SER F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 113 removed outlier: 3.595A pdb=" N LEU F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 120 removed outlier: 4.390A pdb=" N ASN F 119 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER F 120 " --> pdb=" O TYR F 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 116 through 120' Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 168 through 184 removed outlier: 3.534A pdb=" N LYS F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.321A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 220 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 Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 340 through 348 removed outlier: 4.126A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.936A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 230 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 234 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.936A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 230 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 234 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.936A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 230 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.935A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET D 230 " --> pdb=" O CYS D 187 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 removed outlier: 3.936A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET E 230 " --> pdb=" O CYS E 187 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 removed outlier: 3.916A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP F 192 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET F 230 " --> pdb=" O CYS F 187 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA F 234 " --> pdb=" O ILE F 191 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2076 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: 2.43 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2475 1.32 - 1.44: 3285 1.44 - 1.56: 8339 1.56 - 1.69: 33 1.69 - 1.81: 124 Bond restraints: 14256 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.48e+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 6.36e+01 bond pdb=" C4 ATP E 401 " pdb=" C5 ATP E 401 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.32e+01 bond pdb=" C4 ATP F 401 " pdb=" C5 ATP F 401 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP D 401 " pdb=" C5 ATP D 401 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.15e+01 ... (remaining 14251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 18882 3.56 - 7.12: 324 7.12 - 10.68: 45 10.68 - 14.24: 8 14.24 - 17.79: 6 Bond angle restraints: 19265 Sorted by residual: angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 122.08 17.79 1.00e+00 1.00e+00 3.17e+02 angle pdb=" PB ATP D 401 " pdb=" O3B ATP D 401 " pdb=" PG ATP D 401 " ideal model delta sigma weight residual 139.87 122.08 17.79 1.00e+00 1.00e+00 3.16e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 122.13 17.74 1.00e+00 1.00e+00 3.15e+02 angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 122.24 17.63 1.00e+00 1.00e+00 3.11e+02 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 122.35 17.52 1.00e+00 1.00e+00 3.07e+02 ... (remaining 19260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7765 17.97 - 35.94: 860 35.94 - 53.91: 228 53.91 - 71.88: 52 71.88 - 89.85: 50 Dihedral angle restraints: 8955 sinusoidal: 3824 harmonic: 5131 Sorted by residual: dihedral pdb=" CA THR B 274 " pdb=" C THR B 274 " pdb=" N LYS B 275 " pdb=" CA LYS B 275 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR F 274 " pdb=" C THR F 274 " pdb=" N LYS F 275 " pdb=" CA LYS F 275 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C THR C 274 " pdb=" N THR C 274 " pdb=" CA THR C 274 " pdb=" CB THR C 274 " ideal model delta harmonic sigma weight residual -122.00 -111.96 -10.04 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 8952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1849 0.080 - 0.160: 300 0.160 - 0.241: 43 0.241 - 0.321: 9 0.321 - 0.401: 8 Chirality restraints: 2209 Sorted by residual: chirality pdb=" CB VAL F 107 " pdb=" CA VAL F 107 " pdb=" CG1 VAL F 107 " pdb=" CG2 VAL F 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA GLU C 105 " pdb=" N GLU C 105 " pdb=" C GLU C 105 " pdb=" CB GLU C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA GLU B 105 " pdb=" N GLU B 105 " pdb=" C GLU B 105 " pdb=" CB GLU B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 2206 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 90 " -0.022 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE B 90 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE B 90 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 90 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE B 90 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 90 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 90 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 90 " 0.022 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE C 90 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE C 90 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 90 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE C 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 90 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 90 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 90 " -0.022 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE F 90 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE F 90 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE F 90 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE F 90 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 90 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 90 " 0.001 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 117 2.61 - 3.19: 12239 3.19 - 3.76: 23504 3.76 - 4.33: 32843 4.33 - 4.90: 52725 Nonbonded interactions: 121428 Sorted by model distance: nonbonded pdb=" OG1 THR E 140 " pdb="MG MG E 402 " model vdw 2.044 2.170 nonbonded pdb=" OG1 THR C 140 " pdb="MG MG C 402 " model vdw 2.050 2.170 nonbonded pdb=" OG1 THR D 140 " pdb="MG MG D 402 " model vdw 2.077 2.170 nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 402 " model vdw 2.079 2.170 nonbonded pdb=" OG1 THR F 140 " pdb="MG MG F 402 " model vdw 2.106 2.170 ... (remaining 121423 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 402)) selection = (chain 'B' and (resid 51 through 73 or resid 75 through 313 or resid 339 through \ 349 or resid 401 through 402)) selection = (chain 'C' and (resid 51 through 73 or resid 75 through 313 or resid 339 through \ 349 or resid 401 through 402)) selection = (chain 'D' and (resid 51 through 73 or resid 75 through 313 or resid 339 through \ 349 or resid 401 through 402)) selection = (chain 'E' and (resid 51 through 73 or resid 75 through 313 or resid 339 through \ 349 or resid 401 through 402)) selection = (chain 'F' and (resid 51 through 73 or resid 75 through 313 or resid 339 through \ 349 or resid 401 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: 12.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.440 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:8.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 0.112 14256 Z= 0.455 Angle : 1.168 17.794 19265 Z= 0.771 Chirality : 0.065 0.401 2209 Planarity : 0.006 0.056 2416 Dihedral : 17.704 89.846 5611 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.34 % Allowed : 9.49 % Favored : 88.17 % 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: -0.63 (0.20), residues: 1720 helix: -0.25 (0.16), residues: 965 sheet: -0.89 (0.38), residues: 159 loop : -0.22 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 237 TYR 0.016 0.003 TYR D 167 PHE 0.065 0.003 PHE B 90 TRP 0.014 0.002 TRP B 166 HIS 0.005 0.002 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00661 (14256) covalent geometry : angle 1.16833 (19265) hydrogen bonds : bond 0.17819 ( 726) hydrogen bonds : angle 6.55664 ( 2076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 354 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 149 GLU cc_start: 0.6915 (pt0) cc_final: 0.6649 (pt0) REVERT: A 224 LEU cc_start: 0.8623 (mt) cc_final: 0.8010 (mt) REVERT: A 243 ASP cc_start: 0.6727 (m-30) cc_final: 0.6399 (t0) REVERT: C 277 ASP cc_start: 0.6610 (t70) cc_final: 0.6010 (t0) REVERT: D 236 ASN cc_start: 0.7508 (m-40) cc_final: 0.7285 (m-40) REVERT: D 284 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7525 (tp40) REVERT: D 288 ASP cc_start: 0.7479 (m-30) cc_final: 0.7239 (m-30) REVERT: E 297 ASP cc_start: 0.8411 (m-30) cc_final: 0.8140 (m-30) REVERT: F 273 ASP cc_start: 0.8271 (m-30) cc_final: 0.7340 (t0) outliers start: 34 outliers final: 8 residues processed: 368 average time/residue: 0.6134 time to fit residues: 246.1919 Evaluate side-chains 233 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 225 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 153 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN E 319 GLN F 236 ASN F 262 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.177482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134890 restraints weight = 30815.352| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.88 r_work: 0.3140 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14256 Z= 0.149 Angle : 0.626 8.700 19265 Z= 0.306 Chirality : 0.044 0.142 2209 Planarity : 0.005 0.048 2416 Dihedral : 11.756 81.671 2095 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.77 % Allowed : 16.24 % Favored : 79.99 % 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: 0.14 (0.20), residues: 1720 helix: 0.36 (0.16), residues: 981 sheet: -1.08 (0.37), residues: 164 loop : 0.31 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 263 TYR 0.016 0.001 TYR D 167 PHE 0.019 0.002 PHE B 90 TRP 0.008 0.001 TRP B 166 HIS 0.002 0.000 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00349 (14256) covalent geometry : angle 0.62585 (19265) hydrogen bonds : bond 0.03677 ( 726) hydrogen bonds : angle 5.25584 ( 2076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.7988 (pp) cc_final: 0.7731 (pp) REVERT: A 78 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7596 (p) REVERT: A 149 GLU cc_start: 0.6943 (pt0) cc_final: 0.6493 (pt0) REVERT: A 205 ASP cc_start: 0.7891 (m-30) cc_final: 0.7524 (m-30) REVERT: A 224 LEU cc_start: 0.8397 (mt) cc_final: 0.8110 (mm) REVERT: A 243 ASP cc_start: 0.7366 (m-30) cc_final: 0.6810 (t0) REVERT: A 263 ARG cc_start: 0.5768 (mtm110) cc_final: 0.4952 (ttt180) REVERT: B 260 SER cc_start: 0.7921 (m) cc_final: 0.7170 (t) REVERT: C 53 GLN cc_start: 0.8110 (mm110) cc_final: 0.7777 (mm-40) REVERT: C 277 ASP cc_start: 0.6721 (t70) cc_final: 0.6183 (t0) REVERT: C 282 ASP cc_start: 0.7219 (t0) cc_final: 0.6228 (p0) REVERT: C 284 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7507 (tp-100) REVERT: C 300 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: D 92 ASP cc_start: 0.7811 (m-30) cc_final: 0.7602 (m-30) REVERT: D 204 THR cc_start: 0.8939 (p) cc_final: 0.8703 (t) REVERT: D 262 GLN cc_start: 0.7677 (mt0) cc_final: 0.7457 (tt0) REVERT: D 284 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7196 (tp40) REVERT: D 288 ASP cc_start: 0.7559 (m-30) cc_final: 0.7129 (m-30) REVERT: E 73 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: E 85 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: E 101 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7522 (p) REVERT: E 278 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6936 (mm-30) REVERT: F 59 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7437 (tmmt) REVERT: F 149 GLU cc_start: 0.7305 (pt0) cc_final: 0.6999 (pt0) REVERT: F 177 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7782 (ptp) REVERT: F 217 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7166 (mmt) REVERT: F 273 ASP cc_start: 0.7812 (m-30) cc_final: 0.7025 (t0) REVERT: F 315 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7790 (mtmm) outliers start: 56 outliers final: 10 residues processed: 270 average time/residue: 0.5526 time to fit residues: 164.8512 Evaluate side-chains 228 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 315 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 97 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 143 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 236 ASN C 236 ASN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.167487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123032 restraints weight = 29598.907| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.63 r_work: 0.3010 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14256 Z= 0.193 Angle : 0.626 10.459 19265 Z= 0.305 Chirality : 0.045 0.158 2209 Planarity : 0.005 0.058 2416 Dihedral : 11.662 80.299 2087 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.38 % Allowed : 18.39 % Favored : 78.23 % 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: 0.58 (0.20), residues: 1720 helix: 0.72 (0.16), residues: 971 sheet: -1.07 (0.35), residues: 168 loop : 0.58 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 263 TYR 0.022 0.002 TYR E 264 PHE 0.024 0.002 PHE B 178 TRP 0.012 0.002 TRP B 166 HIS 0.004 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00470 (14256) covalent geometry : angle 0.62579 (19265) hydrogen bonds : bond 0.03510 ( 726) hydrogen bonds : angle 5.02434 ( 2076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 78 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7516 (p) REVERT: A 149 GLU cc_start: 0.6863 (pt0) cc_final: 0.6404 (pt0) REVERT: A 205 ASP cc_start: 0.7944 (m-30) cc_final: 0.7663 (m-30) REVERT: A 224 LEU cc_start: 0.8419 (mt) cc_final: 0.8200 (mm) REVERT: A 243 ASP cc_start: 0.7643 (m-30) cc_final: 0.6969 (t0) REVERT: A 252 ARG cc_start: 0.7362 (tpp80) cc_final: 0.7098 (tpp80) REVERT: A 263 ARG cc_start: 0.5819 (mtm110) cc_final: 0.5577 (mtm110) REVERT: A 298 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5504 (mt) REVERT: B 149 GLU cc_start: 0.8357 (pt0) cc_final: 0.8111 (pt0) REVERT: C 262 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: C 277 ASP cc_start: 0.6763 (t70) cc_final: 0.6190 (t0) REVERT: D 92 ASP cc_start: 0.7967 (m-30) cc_final: 0.7477 (m-30) REVERT: D 175 ASP cc_start: 0.8417 (t70) cc_final: 0.8194 (t0) REVERT: D 204 THR cc_start: 0.8936 (p) cc_final: 0.8670 (t) REVERT: D 243 ASP cc_start: 0.8028 (m-30) cc_final: 0.7638 (m-30) REVERT: D 282 ASP cc_start: 0.7303 (t0) cc_final: 0.6592 (t0) REVERT: D 284 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7228 (tp40) REVERT: D 285 LEU cc_start: 0.7848 (tt) cc_final: 0.7522 (tp) REVERT: D 288 ASP cc_start: 0.7609 (m-30) cc_final: 0.7276 (m-30) REVERT: E 53 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.6053 (mp10) REVERT: E 261 ASP cc_start: 0.7586 (p0) cc_final: 0.6755 (m-30) REVERT: F 52 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7237 (tt) REVERT: F 149 GLU cc_start: 0.7551 (pt0) cc_final: 0.7250 (pt0) REVERT: F 217 MET cc_start: 0.7627 (mmm) cc_final: 0.7369 (mmt) REVERT: F 256 SER cc_start: 0.7735 (p) cc_final: 0.7286 (m) REVERT: F 273 ASP cc_start: 0.7725 (m-30) cc_final: 0.6967 (t0) REVERT: F 315 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7779 (mtmm) REVERT: F 338 PRO cc_start: 0.7390 (Cg_exo) cc_final: 0.6823 (Cg_endo) outliers start: 50 outliers final: 10 residues processed: 258 average time/residue: 0.5025 time to fit residues: 142.0992 Evaluate side-chains 215 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 315 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 167 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 171 ASN E 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.168942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118245 restraints weight = 26076.280| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.51 r_work: 0.3102 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14256 Z= 0.131 Angle : 0.548 9.059 19265 Z= 0.267 Chirality : 0.042 0.137 2209 Planarity : 0.004 0.038 2416 Dihedral : 11.397 83.410 2086 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.92 % Allowed : 20.27 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.20), residues: 1720 helix: 1.00 (0.16), residues: 970 sheet: -1.18 (0.33), residues: 186 loop : 0.78 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 199 TYR 0.019 0.001 TYR E 264 PHE 0.013 0.001 PHE F 197 TRP 0.005 0.001 TRP B 166 HIS 0.001 0.000 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00316 (14256) covalent geometry : angle 0.54819 (19265) hydrogen bonds : bond 0.03009 ( 726) hydrogen bonds : angle 4.87524 ( 2076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 60 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.4978 (tmm160) REVERT: A 78 SER cc_start: 0.7801 (OUTLIER) cc_final: 0.7516 (p) REVERT: A 90 PHE cc_start: 0.6176 (m-80) cc_final: 0.5942 (m-80) REVERT: A 141 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6307 (mmm) REVERT: A 149 GLU cc_start: 0.6838 (pt0) cc_final: 0.6426 (pt0) REVERT: A 205 ASP cc_start: 0.8032 (m-30) cc_final: 0.7707 (m-30) REVERT: A 224 LEU cc_start: 0.8371 (mt) cc_final: 0.8127 (mm) REVERT: A 243 ASP cc_start: 0.7841 (m-30) cc_final: 0.7530 (m-30) REVERT: A 252 ARG cc_start: 0.7339 (tpp80) cc_final: 0.7056 (tpp80) REVERT: A 263 ARG cc_start: 0.5863 (mtm110) cc_final: 0.5574 (mtm110) REVERT: B 149 GLU cc_start: 0.8407 (pt0) cc_final: 0.8159 (pt0) REVERT: C 115 GLU cc_start: 0.7523 (pm20) cc_final: 0.7306 (pp20) REVERT: C 159 MET cc_start: 0.8397 (tpp) cc_final: 0.8136 (tpt) REVERT: C 262 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: C 277 ASP cc_start: 0.6791 (t70) cc_final: 0.6166 (t0) REVERT: C 284 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7393 (tp-100) REVERT: C 300 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: D 92 ASP cc_start: 0.8026 (m-30) cc_final: 0.7501 (m-30) REVERT: D 175 ASP cc_start: 0.8444 (t70) cc_final: 0.8229 (t0) REVERT: D 204 THR cc_start: 0.8894 (p) cc_final: 0.8642 (t) REVERT: D 284 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7310 (tp40) REVERT: D 288 ASP cc_start: 0.7716 (m-30) cc_final: 0.7465 (m-30) REVERT: E 53 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.6131 (mp10) REVERT: E 261 ASP cc_start: 0.7651 (p0) cc_final: 0.6955 (m-30) REVERT: E 278 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6850 (mm-30) REVERT: F 217 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7392 (mmt) REVERT: F 273 ASP cc_start: 0.7716 (m-30) cc_final: 0.6920 (t0) outliers start: 43 outliers final: 9 residues processed: 239 average time/residue: 0.5544 time to fit residues: 145.7179 Evaluate side-chains 217 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 217 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 140 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN D 236 ASN E 50 GLN E 236 ASN E 262 GLN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.162089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119387 restraints weight = 35621.356| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.58 r_work: 0.2866 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14256 Z= 0.242 Angle : 0.636 8.993 19265 Z= 0.308 Chirality : 0.046 0.160 2209 Planarity : 0.005 0.074 2416 Dihedral : 11.579 86.165 2086 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.31 % Allowed : 19.95 % Favored : 76.74 % 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: 0.78 (0.20), residues: 1720 helix: 0.89 (0.16), residues: 964 sheet: -1.24 (0.33), residues: 202 loop : 0.87 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 263 TYR 0.022 0.002 TYR E 264 PHE 0.019 0.002 PHE B 178 TRP 0.013 0.002 TRP D 220 HIS 0.003 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00600 (14256) covalent geometry : angle 0.63645 (19265) hydrogen bonds : bond 0.03505 ( 726) hydrogen bonds : angle 5.02018 ( 2076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.595 Fit side-chains REVERT: A 60 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.4940 (tmm160) REVERT: A 78 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7477 (p) REVERT: A 141 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6378 (mtp) REVERT: A 149 GLU cc_start: 0.6787 (pt0) cc_final: 0.6442 (pt0) REVERT: A 205 ASP cc_start: 0.8111 (m-30) cc_final: 0.7569 (m-30) REVERT: A 224 LEU cc_start: 0.8475 (mt) cc_final: 0.8193 (mm) REVERT: A 243 ASP cc_start: 0.7875 (m-30) cc_final: 0.7150 (t0) REVERT: A 252 ARG cc_start: 0.7578 (tpp80) cc_final: 0.7084 (tpp80) REVERT: A 263 ARG cc_start: 0.5909 (mtm110) cc_final: 0.5177 (ttt180) REVERT: A 265 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6322 (mtmm) REVERT: B 108 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8203 (mt) REVERT: B 113 MET cc_start: 0.8491 (mtt) cc_final: 0.8122 (mtm) REVERT: B 149 GLU cc_start: 0.8485 (pt0) cc_final: 0.8242 (pt0) REVERT: C 199 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7735 (mtm-85) REVERT: C 262 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: C 282 ASP cc_start: 0.7632 (t0) cc_final: 0.6393 (p0) REVERT: C 300 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: C 342 LYS cc_start: 0.7346 (ptpt) cc_final: 0.7104 (pmtt) REVERT: D 92 ASP cc_start: 0.8145 (m-30) cc_final: 0.7600 (m-30) REVERT: D 163 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8158 (mtt) REVERT: D 175 ASP cc_start: 0.8528 (t70) cc_final: 0.8281 (t0) REVERT: D 204 THR cc_start: 0.8939 (p) cc_final: 0.8667 (t) REVERT: D 284 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7416 (tp40) REVERT: E 53 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.5949 (mp10) REVERT: E 91 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7506 (mm-40) REVERT: E 182 ASN cc_start: 0.8936 (m-40) cc_final: 0.8734 (m110) REVERT: E 261 ASP cc_start: 0.7602 (p0) cc_final: 0.7018 (m-30) REVERT: E 284 GLN cc_start: 0.8316 (tp-100) cc_final: 0.7925 (tp-100) REVERT: F 217 MET cc_start: 0.7659 (mmm) cc_final: 0.7412 (tpt) REVERT: F 273 ASP cc_start: 0.7714 (m-30) cc_final: 0.6957 (t0) REVERT: F 338 PRO cc_start: 0.7558 (Cg_exo) cc_final: 0.7012 (Cg_endo) outliers start: 49 outliers final: 14 residues processed: 255 average time/residue: 0.6182 time to fit residues: 172.4196 Evaluate side-chains 230 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 236 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 236 ASN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.162994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111229 restraints weight = 29590.842| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.68 r_work: 0.3000 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14256 Z= 0.188 Angle : 0.591 9.430 19265 Z= 0.286 Chirality : 0.044 0.165 2209 Planarity : 0.004 0.048 2416 Dihedral : 11.546 89.500 2086 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.05 % Allowed : 21.12 % Favored : 75.83 % 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: 0.85 (0.20), residues: 1720 helix: 0.94 (0.16), residues: 959 sheet: -1.21 (0.33), residues: 198 loop : 0.92 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 199 TYR 0.021 0.002 TYR E 264 PHE 0.014 0.001 PHE B 178 TRP 0.008 0.001 TRP D 220 HIS 0.002 0.001 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00461 (14256) covalent geometry : angle 0.59136 (19265) hydrogen bonds : bond 0.03230 ( 726) hydrogen bonds : angle 4.95682 ( 2076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.645 Fit side-chains REVERT: A 60 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.4915 (tmm160) REVERT: A 73 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: A 78 SER cc_start: 0.7813 (OUTLIER) cc_final: 0.7511 (p) REVERT: A 141 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6586 (ttm) REVERT: A 149 GLU cc_start: 0.6808 (pt0) cc_final: 0.6396 (pt0) REVERT: A 205 ASP cc_start: 0.8188 (m-30) cc_final: 0.7618 (m-30) REVERT: A 224 LEU cc_start: 0.8453 (mt) cc_final: 0.8169 (mm) REVERT: A 243 ASP cc_start: 0.7953 (m-30) cc_final: 0.7226 (t0) REVERT: A 252 ARG cc_start: 0.7580 (tpp80) cc_final: 0.7047 (tpp80) REVERT: A 263 ARG cc_start: 0.5864 (mtm110) cc_final: 0.5185 (ttt180) REVERT: B 108 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 113 MET cc_start: 0.8481 (mtt) cc_final: 0.8200 (mtm) REVERT: B 149 GLU cc_start: 0.8486 (pt0) cc_final: 0.8255 (pt0) REVERT: C 262 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7728 (mt0) REVERT: C 284 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7433 (tp-100) REVERT: C 300 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: D 92 ASP cc_start: 0.8157 (m-30) cc_final: 0.7628 (m-30) REVERT: D 175 ASP cc_start: 0.8551 (t70) cc_final: 0.8309 (t0) REVERT: D 204 THR cc_start: 0.8939 (p) cc_final: 0.8687 (t) REVERT: D 284 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7439 (tp40) REVERT: E 53 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.5983 (mp10) REVERT: E 73 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8114 (mt-10) REVERT: E 91 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7532 (mm-40) REVERT: E 261 ASP cc_start: 0.7616 (p0) cc_final: 0.7085 (m-30) REVERT: E 284 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7914 (tp-100) REVERT: F 217 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7431 (tpt) REVERT: F 273 ASP cc_start: 0.7666 (m-30) cc_final: 0.6931 (t0) REVERT: F 338 PRO cc_start: 0.7570 (Cg_exo) cc_final: 0.7025 (Cg_endo) outliers start: 45 outliers final: 13 residues processed: 235 average time/residue: 0.5630 time to fit residues: 144.8566 Evaluate side-chains 223 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 217 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 60 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 236 ASN E 50 GLN E 262 GLN ** F 153 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 = 0.3822 r_free = 0.3822 target = 0.164710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113650 restraints weight = 26099.317| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.54 r_work: 0.3021 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14256 Z= 0.137 Angle : 0.558 9.456 19265 Z= 0.271 Chirality : 0.042 0.138 2209 Planarity : 0.004 0.042 2416 Dihedral : 11.367 87.208 2086 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.60 % Allowed : 21.77 % Favored : 75.63 % 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: 1.00 (0.20), residues: 1720 helix: 1.04 (0.17), residues: 971 sheet: -1.12 (0.33), residues: 197 loop : 1.02 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 199 TYR 0.022 0.001 TYR E 264 PHE 0.015 0.001 PHE A 90 TRP 0.005 0.001 TRP D 220 HIS 0.001 0.001 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00332 (14256) covalent geometry : angle 0.55804 (19265) hydrogen bonds : bond 0.02983 ( 726) hydrogen bonds : angle 4.83351 ( 2076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.568 Fit side-chains REVERT: A 78 SER cc_start: 0.7748 (OUTLIER) cc_final: 0.7433 (p) REVERT: A 149 GLU cc_start: 0.6799 (pt0) cc_final: 0.6307 (pt0) REVERT: A 203 SER cc_start: 0.8241 (OUTLIER) cc_final: 0.7802 (p) REVERT: A 205 ASP cc_start: 0.8152 (m-30) cc_final: 0.7562 (m-30) REVERT: A 224 LEU cc_start: 0.8364 (mt) cc_final: 0.8096 (mm) REVERT: A 243 ASP cc_start: 0.7939 (m-30) cc_final: 0.7232 (t0) REVERT: A 252 ARG cc_start: 0.7516 (tpp80) cc_final: 0.7173 (tpp80) REVERT: A 263 ARG cc_start: 0.5843 (mtm110) cc_final: 0.5185 (ttt180) REVERT: B 108 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8241 (mt) REVERT: B 113 MET cc_start: 0.8454 (mtt) cc_final: 0.8186 (mtm) REVERT: B 149 GLU cc_start: 0.8462 (pt0) cc_final: 0.8230 (pt0) REVERT: C 55 GLU cc_start: 0.7650 (pt0) cc_final: 0.6975 (mm-30) REVERT: C 262 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: C 282 ASP cc_start: 0.7565 (t0) cc_final: 0.6469 (p0) REVERT: C 284 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7430 (tp-100) REVERT: C 300 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: D 92 ASP cc_start: 0.8093 (m-30) cc_final: 0.7592 (m-30) REVERT: D 163 MET cc_start: 0.8517 (mmm) cc_final: 0.8285 (mtt) REVERT: D 175 ASP cc_start: 0.8475 (t70) cc_final: 0.8247 (t0) REVERT: D 204 THR cc_start: 0.8916 (p) cc_final: 0.8663 (t) REVERT: D 284 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7407 (tp40) REVERT: E 53 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.5964 (mp10) REVERT: E 73 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: E 91 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7531 (mm-40) REVERT: E 261 ASP cc_start: 0.7598 (p0) cc_final: 0.7196 (m-30) REVERT: E 278 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6915 (mm-30) REVERT: E 284 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7874 (tp-100) REVERT: E 311 LYS cc_start: 0.7362 (ttmm) cc_final: 0.6449 (pttm) REVERT: F 157 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8975 (tp) REVERT: F 273 ASP cc_start: 0.7578 (m-30) cc_final: 0.6881 (t0) REVERT: F 338 PRO cc_start: 0.7514 (Cg_exo) cc_final: 0.6965 (Cg_endo) outliers start: 38 outliers final: 11 residues processed: 233 average time/residue: 0.5544 time to fit residues: 142.1472 Evaluate side-chains 230 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 157 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 166 optimal weight: 0.0010 chunk 95 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN D 284 GLN E 50 GLN E 262 GLN ** F 153 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 = 0.3833 r_free = 0.3833 target = 0.165668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114509 restraints weight = 27306.042| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.60 r_work: 0.3032 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14256 Z= 0.125 Angle : 0.549 9.154 19265 Z= 0.266 Chirality : 0.042 0.172 2209 Planarity : 0.004 0.043 2416 Dihedral : 11.253 84.900 2086 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.08 % Allowed : 22.61 % Favored : 75.31 % 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: 1.13 (0.21), residues: 1720 helix: 1.13 (0.17), residues: 972 sheet: -1.12 (0.33), residues: 199 loop : 1.14 (0.29), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 199 TYR 0.022 0.001 TYR E 264 PHE 0.015 0.001 PHE F 197 TRP 0.006 0.001 TRP A 54 HIS 0.003 0.000 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00301 (14256) covalent geometry : angle 0.54933 (19265) hydrogen bonds : bond 0.02889 ( 726) hydrogen bonds : angle 4.78794 ( 2076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.498 Fit side-chains REVERT: A 73 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: A 78 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7417 (p) REVERT: A 149 GLU cc_start: 0.6723 (pt0) cc_final: 0.6316 (pt0) REVERT: A 203 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7820 (p) REVERT: A 205 ASP cc_start: 0.8107 (m-30) cc_final: 0.7503 (m-30) REVERT: A 224 LEU cc_start: 0.8320 (mt) cc_final: 0.8080 (mm) REVERT: A 243 ASP cc_start: 0.7961 (m-30) cc_final: 0.7219 (t0) REVERT: A 252 ARG cc_start: 0.7486 (tpp80) cc_final: 0.7162 (tpp80) REVERT: A 263 ARG cc_start: 0.5813 (mtm110) cc_final: 0.5170 (ttt180) REVERT: B 108 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8230 (mt) REVERT: B 113 MET cc_start: 0.8420 (mtt) cc_final: 0.8151 (mtm) REVERT: B 149 GLU cc_start: 0.8434 (pt0) cc_final: 0.8196 (pt0) REVERT: C 55 GLU cc_start: 0.7657 (pt0) cc_final: 0.6977 (mm-30) REVERT: C 122 LEU cc_start: 0.8051 (pt) cc_final: 0.7835 (pp) REVERT: C 262 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: C 282 ASP cc_start: 0.7533 (t0) cc_final: 0.6402 (p0) REVERT: C 284 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7447 (tp-100) REVERT: C 300 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: D 92 ASP cc_start: 0.8073 (m-30) cc_final: 0.7559 (m-30) REVERT: D 163 MET cc_start: 0.8468 (mmm) cc_final: 0.8193 (mtt) REVERT: D 175 ASP cc_start: 0.8460 (t70) cc_final: 0.8236 (t0) REVERT: D 204 THR cc_start: 0.8898 (p) cc_final: 0.8643 (t) REVERT: D 284 GLN cc_start: 0.7714 (tp40) cc_final: 0.7501 (tp40) REVERT: D 342 LYS cc_start: 0.7516 (mmtt) cc_final: 0.7079 (mtpp) REVERT: E 53 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.5953 (mp10) REVERT: E 73 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: E 91 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7536 (mm-40) REVERT: E 124 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7498 (mt0) REVERT: E 261 ASP cc_start: 0.7602 (p0) cc_final: 0.7277 (m-30) REVERT: E 278 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6910 (mm-30) REVERT: E 284 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7845 (tp-100) REVERT: E 311 LYS cc_start: 0.7342 (ttmm) cc_final: 0.6469 (pttm) REVERT: F 273 ASP cc_start: 0.7551 (m-30) cc_final: 0.6862 (t0) REVERT: F 338 PRO cc_start: 0.7484 (Cg_exo) cc_final: 0.6933 (Cg_endo) outliers start: 30 outliers final: 11 residues processed: 232 average time/residue: 0.5294 time to fit residues: 135.0835 Evaluate side-chains 232 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN E 50 GLN E 262 GLN ** F 153 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 = 0.3827 r_free = 0.3827 target = 0.165299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123562 restraints weight = 35338.875| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.76 r_work: 0.2955 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14256 Z= 0.137 Angle : 0.569 9.809 19265 Z= 0.274 Chirality : 0.042 0.203 2209 Planarity : 0.004 0.043 2416 Dihedral : 11.186 85.587 2086 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.01 % Allowed : 23.07 % Favored : 74.92 % 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: 1.13 (0.21), residues: 1720 helix: 1.17 (0.17), residues: 972 sheet: -1.20 (0.32), residues: 201 loop : 1.09 (0.29), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 199 TYR 0.010 0.001 TYR B 109 PHE 0.014 0.001 PHE A 90 TRP 0.008 0.001 TRP A 54 HIS 0.006 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00333 (14256) covalent geometry : angle 0.56862 (19265) hydrogen bonds : bond 0.02950 ( 726) hydrogen bonds : angle 4.81996 ( 2076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: A 78 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7469 (p) REVERT: A 124 GLN cc_start: 0.8227 (tp40) cc_final: 0.7617 (mm-40) REVERT: A 141 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6661 (mtp) REVERT: A 149 GLU cc_start: 0.6717 (pt0) cc_final: 0.6301 (pt0) REVERT: A 203 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 205 ASP cc_start: 0.8076 (m-30) cc_final: 0.7512 (m-30) REVERT: A 215 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: A 224 LEU cc_start: 0.8331 (mt) cc_final: 0.8094 (mm) REVERT: A 243 ASP cc_start: 0.7965 (m-30) cc_final: 0.7242 (t0) REVERT: A 263 ARG cc_start: 0.5820 (mtm110) cc_final: 0.5186 (ttt180) REVERT: B 108 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8314 (mt) REVERT: B 113 MET cc_start: 0.8473 (mtt) cc_final: 0.8209 (mtm) REVERT: B 149 GLU cc_start: 0.8405 (pt0) cc_final: 0.8181 (pt0) REVERT: C 55 GLU cc_start: 0.7714 (pt0) cc_final: 0.7087 (mm-30) REVERT: C 122 LEU cc_start: 0.8050 (pt) cc_final: 0.7828 (pp) REVERT: C 262 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: C 282 ASP cc_start: 0.7601 (t0) cc_final: 0.6519 (p0) REVERT: C 284 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7505 (tp-100) REVERT: C 300 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: D 92 ASP cc_start: 0.8023 (m-30) cc_final: 0.7524 (m-30) REVERT: D 163 MET cc_start: 0.8381 (mmm) cc_final: 0.8042 (mtt) REVERT: D 175 ASP cc_start: 0.8411 (t70) cc_final: 0.8196 (t0) REVERT: D 204 THR cc_start: 0.8909 (p) cc_final: 0.8651 (t) REVERT: D 342 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7144 (mtpp) REVERT: E 53 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.6034 (mp10) REVERT: E 73 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: E 91 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7580 (mm-40) REVERT: E 124 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7544 (mt0) REVERT: E 261 ASP cc_start: 0.7578 (p0) cc_final: 0.7334 (m-30) REVERT: E 278 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6960 (mm-30) REVERT: E 284 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7899 (tp-100) REVERT: E 311 LYS cc_start: 0.7431 (ttmm) cc_final: 0.6576 (pttm) REVERT: F 256 SER cc_start: 0.7728 (p) cc_final: 0.7260 (m) REVERT: F 273 ASP cc_start: 0.7553 (m-30) cc_final: 0.6880 (t0) REVERT: F 304 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7343 (mm-30) REVERT: F 338 PRO cc_start: 0.7519 (Cg_exo) cc_final: 0.6967 (Cg_endo) outliers start: 29 outliers final: 13 residues processed: 232 average time/residue: 0.5535 time to fit residues: 141.5579 Evaluate side-chains 236 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 165 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 165 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN E 50 GLN E 262 GLN ** F 153 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 = 0.3819 r_free = 0.3819 target = 0.164667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120139 restraints weight = 28984.195| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.40 r_work: 0.2954 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14256 Z= 0.162 Angle : 0.588 9.650 19265 Z= 0.283 Chirality : 0.043 0.232 2209 Planarity : 0.004 0.045 2416 Dihedral : 11.235 86.582 2086 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.08 % Allowed : 22.94 % Favored : 74.98 % 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: 1.08 (0.21), residues: 1720 helix: 1.14 (0.17), residues: 970 sheet: -1.21 (0.33), residues: 201 loop : 1.05 (0.29), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 199 TYR 0.024 0.001 TYR E 264 PHE 0.016 0.001 PHE F 197 TRP 0.007 0.001 TRP D 220 HIS 0.002 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00397 (14256) covalent geometry : angle 0.58762 (19265) hydrogen bonds : bond 0.03063 ( 726) hydrogen bonds : angle 4.86668 ( 2076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.606 Fit side-chains REVERT: A 73 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: A 78 SER cc_start: 0.7751 (OUTLIER) cc_final: 0.7458 (p) REVERT: A 124 GLN cc_start: 0.8202 (tp40) cc_final: 0.7644 (mm-40) REVERT: A 141 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6785 (mtp) REVERT: A 149 GLU cc_start: 0.6769 (pt0) cc_final: 0.6353 (pt0) REVERT: A 203 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7891 (p) REVERT: A 205 ASP cc_start: 0.8093 (m-30) cc_final: 0.7517 (m-30) REVERT: A 215 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: A 243 ASP cc_start: 0.7911 (m-30) cc_final: 0.7191 (t0) REVERT: A 263 ARG cc_start: 0.5824 (mtm110) cc_final: 0.5199 (ttt180) REVERT: B 108 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8263 (mt) REVERT: B 113 MET cc_start: 0.8447 (mtt) cc_final: 0.8150 (mtm) REVERT: B 149 GLU cc_start: 0.8366 (pt0) cc_final: 0.8134 (pt0) REVERT: C 55 GLU cc_start: 0.7678 (pt0) cc_final: 0.7110 (mm-30) REVERT: C 141 MET cc_start: 0.9004 (mmm) cc_final: 0.8622 (tpt) REVERT: C 262 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: C 282 ASP cc_start: 0.7581 (t0) cc_final: 0.6492 (p0) REVERT: C 284 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7479 (tp-100) REVERT: C 300 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: D 92 ASP cc_start: 0.7984 (m-30) cc_final: 0.7497 (m-30) REVERT: D 163 MET cc_start: 0.8285 (mmm) cc_final: 0.7841 (mtt) REVERT: D 175 ASP cc_start: 0.8343 (t70) cc_final: 0.8140 (t0) REVERT: D 204 THR cc_start: 0.8917 (p) cc_final: 0.8648 (t) REVERT: D 342 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7257 (mtpp) REVERT: E 53 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.5983 (mp10) REVERT: E 73 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: E 91 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7571 (mm-40) REVERT: E 124 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7538 (mt0) REVERT: E 261 ASP cc_start: 0.7514 (p0) cc_final: 0.7314 (m-30) REVERT: E 278 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6957 (mm-30) REVERT: E 284 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7896 (tp-100) REVERT: E 311 LYS cc_start: 0.7435 (ttmm) cc_final: 0.6608 (pttm) REVERT: F 256 SER cc_start: 0.7790 (p) cc_final: 0.7313 (m) REVERT: F 273 ASP cc_start: 0.7480 (m-30) cc_final: 0.6883 (t0) REVERT: F 284 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7412 (tp-100) REVERT: F 304 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7267 (mm-30) outliers start: 30 outliers final: 14 residues processed: 234 average time/residue: 0.5786 time to fit residues: 148.9228 Evaluate side-chains 237 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 165 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN E 262 GLN ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.165890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123118 restraints weight = 37745.831| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.69 r_work: 0.2982 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14256 Z= 0.133 Angle : 0.576 9.928 19265 Z= 0.278 Chirality : 0.042 0.215 2209 Planarity : 0.004 0.043 2416 Dihedral : 11.160 86.881 2086 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.88 % Allowed : 23.39 % Favored : 74.72 % 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: 1.12 (0.21), residues: 1720 helix: 1.13 (0.17), residues: 978 sheet: -1.14 (0.33), residues: 200 loop : 1.12 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 199 TYR 0.022 0.001 TYR E 264 PHE 0.011 0.001 PHE A 90 TRP 0.010 0.001 TRP A 54 HIS 0.002 0.000 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00322 (14256) covalent geometry : angle 0.57594 (19265) hydrogen bonds : bond 0.02996 ( 726) hydrogen bonds : angle 4.84204 ( 2076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6812.74 seconds wall clock time: 116 minutes 40.94 seconds (7000.94 seconds total)