Starting phenix.real_space_refine on Tue Mar 3 17:47:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c9a_30310/03_2026/7c9a_30310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9a_30310/03_2026/7c9a_30310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7c9a_30310/03_2026/7c9a_30310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9a_30310/03_2026/7c9a_30310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c9a_30310/03_2026/7c9a_30310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9a_30310/03_2026/7c9a_30310.map" } resolution = 3.43 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= 0.002 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 Ca 3 9.91 5 P 27 5.49 5 S 39 5.16 5 C 4674 2.51 5 N 1341 2.21 5 O 1506 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7590 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2375 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2375 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2375 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 2, 'ANP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.51, per 1000 atoms: 0.20 Number of scatterers: 7590 At special positions: 0 Unit cell: (103.32, 84, 115.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 39 16.00 P 27 15.00 O 1506 8.00 N 1341 7.00 C 4674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 242.2 milliseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 49.6% alpha, 12.4% beta 6 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.568A pdb=" N ARG A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 30 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS A 31 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.986A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.679A pdb=" N VAL A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.638A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.554A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 removed outlier: 4.283A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 82' Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.740A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 removed outlier: 3.684A pdb=" N ASP A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.561A pdb=" N CYS A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 141 " --> pdb=" O CYS A 137 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.601A pdb=" N GLY A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.523A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 188 removed outlier: 3.683A pdb=" N ASN A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 209 removed outlier: 4.078A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.521A pdb=" N MET A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.770A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 removed outlier: 3.568A pdb=" N ARG B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS B 31 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.987A pdb=" N VAL B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.679A pdb=" N VAL B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.639A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 77 removed outlier: 3.554A pdb=" N LEU B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 4.283A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 82' Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.740A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.685A pdb=" N ASP B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.560A pdb=" N CYS B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 141 " --> pdb=" O CYS B 137 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.600A pdb=" N GLY B 151 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.523A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 removed outlier: 3.683A pdb=" N ASN B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 209 removed outlier: 4.078A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.521A pdb=" N MET B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.770A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 31 removed outlier: 3.568A pdb=" N ARG C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 29 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 30 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS C 31 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.986A pdb=" N VAL C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.679A pdb=" N VAL C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.639A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.554A pdb=" N LEU C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.284A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 77 through 82' Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.740A pdb=" N GLN C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.685A pdb=" N ASP C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.561A pdb=" N CYS C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.601A pdb=" N GLY C 151 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 removed outlier: 3.523A pdb=" N LEU C 172 " --> pdb=" O PRO C 168 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 removed outlier: 3.683A pdb=" N ASN C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 209 removed outlier: 4.079A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.521A pdb=" N MET C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.770A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.532A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR A 123 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 266 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.531A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR B 123 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 266 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 189 through 193 removed outlier: 3.591A pdb=" N THR C 266 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 122 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU C 300 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU C 124 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU C 302 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE C 126 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LYS C 304 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 330 236 hydrogen bonds defined for protein. 657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2235 1.33 - 1.45: 1238 1.45 - 1.57: 4158 1.57 - 1.69: 47 1.69 - 1.81: 63 Bond restraints: 7741 Sorted by residual: bond pdb=" O3A ANP A 403 " pdb=" PB ANP A 403 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 7736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 10443 4.18 - 8.37: 84 8.37 - 12.55: 7 12.55 - 16.74: 0 16.74 - 20.92: 3 Bond angle restraints: 10537 Sorted by residual: angle pdb=" PB ANP A 403 " pdb=" N3B ANP A 403 " pdb=" PG ANP A 403 " ideal model delta sigma weight residual 126.95 106.03 20.92 3.00e+00 1.11e-01 4.86e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 108.92 18.03 3.00e+00 1.11e-01 3.61e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 108.92 18.03 3.00e+00 1.11e-01 3.61e+01 angle pdb=" CA GLU C 29 " pdb=" CB GLU C 29 " pdb=" CG GLU C 29 " ideal model delta sigma weight residual 114.10 122.93 -8.83 2.00e+00 2.50e-01 1.95e+01 angle pdb=" CA GLU B 29 " pdb=" CB GLU B 29 " pdb=" CG GLU B 29 " ideal model delta sigma weight residual 114.10 122.92 -8.82 2.00e+00 2.50e-01 1.94e+01 ... (remaining 10532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.29: 4390 29.29 - 58.58: 253 58.58 - 87.87: 63 87.87 - 117.16: 1 117.16 - 146.45: 6 Dihedral angle restraints: 4713 sinusoidal: 2058 harmonic: 2655 Sorted by residual: dihedral pdb=" CA ASP C 222 " pdb=" C ASP C 222 " pdb=" N SER C 223 " pdb=" CA SER C 223 " ideal model delta harmonic sigma weight residual -180.00 -61.85 -118.15 0 5.00e+00 4.00e-02 5.58e+02 dihedral pdb=" CA ASP B 222 " pdb=" C ASP B 222 " pdb=" N SER B 223 " pdb=" CA SER B 223 " ideal model delta harmonic sigma weight residual -180.00 -61.86 -118.14 0 5.00e+00 4.00e-02 5.58e+02 dihedral pdb=" CA ASP A 222 " pdb=" C ASP A 222 " pdb=" N SER A 223 " pdb=" CA SER A 223 " ideal model delta harmonic sigma weight residual -180.00 -61.93 -118.07 0 5.00e+00 4.00e-02 5.58e+02 ... (remaining 4710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1010 0.063 - 0.126: 166 0.126 - 0.188: 18 0.188 - 0.251: 0 0.251 - 0.314: 3 Chirality restraints: 1197 Sorted by residual: chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C3' ANP A 403 " pdb=" C2' ANP A 403 " pdb=" C4' ANP A 403 " pdb=" O3' ANP A 403 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1194 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 166 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C PHE B 166 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE B 166 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 167 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 166 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C PHE C 166 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE C 166 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG C 167 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 166 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C PHE A 166 " 0.060 2.00e-02 2.50e+03 pdb=" O PHE A 166 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 167 " -0.020 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 44 2.55 - 3.14: 5155 3.14 - 3.73: 10551 3.73 - 4.31: 15757 4.31 - 4.90: 26283 Nonbonded interactions: 57790 Sorted by model distance: nonbonded pdb=" CE1 PHE A 129 " pdb=" O ALA B 293 " model vdw 1.965 3.340 nonbonded pdb=" CE1 PHE B 129 " pdb=" O ALA C 293 " model vdw 2.003 3.340 nonbonded pdb=" CD1 PHE A 129 " pdb=" O ALA B 293 " model vdw 2.063 3.340 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.078 2.510 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.079 2.510 ... (remaining 57785 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 22 through 336) selection = (chain 'B' and resid 22 through 336) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.970 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 0.149 7741 Z= 0.336 Angle : 1.036 20.922 10537 Z= 0.565 Chirality : 0.048 0.314 1197 Planarity : 0.005 0.039 1293 Dihedral : 19.518 146.452 3015 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.34 % 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: -4.96 (0.20), residues: 921 helix: -5.05 (0.06), residues: 387 sheet: 0.85 (0.48), residues: 120 loop : -2.66 (0.21), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 306 TYR 0.013 0.002 TYR C 315 PHE 0.019 0.002 PHE B 129 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00711 ( 7741) covalent geometry : angle 1.03555 (10537) hydrogen bonds : bond 0.33272 ( 248) hydrogen bonds : angle 10.49934 ( 681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8106 (mmmt) REVERT: B 130 ARG cc_start: 0.7765 (ptt-90) cc_final: 0.7413 (ptp90) REVERT: B 154 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7342 (tp30) REVERT: B 156 LYS cc_start: 0.8757 (mttt) cc_final: 0.8308 (mtpt) REVERT: B 254 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7979 (mtp-110) REVERT: B 285 LYS cc_start: 0.9038 (pttt) cc_final: 0.8745 (ptmm) REVERT: C 237 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8068 (tt0) REVERT: C 285 LYS cc_start: 0.9110 (pttt) cc_final: 0.8877 (ptmm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1451 time to fit residues: 41.0075 Evaluate side-chains 138 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 34 ASN B 242 GLN C 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.125023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.098888 restraints weight = 10841.991| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.30 r_work: 0.2890 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7741 Z= 0.178 Angle : 0.618 8.276 10537 Z= 0.330 Chirality : 0.043 0.158 1197 Planarity : 0.005 0.031 1293 Dihedral : 17.583 152.451 1323 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.48 % Allowed : 14.71 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -3.76 (0.22), residues: 921 helix: -3.58 (0.15), residues: 411 sheet: 0.72 (0.48), residues: 123 loop : -2.15 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 130 TYR 0.013 0.001 TYR A 159 PHE 0.015 0.002 PHE B 129 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7741) covalent geometry : angle 0.61799 (10537) hydrogen bonds : bond 0.04002 ( 248) hydrogen bonds : angle 5.55865 ( 681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.220 Fit side-chains REVERT: A 29 GLU cc_start: 0.7756 (mp0) cc_final: 0.7316 (mm-30) REVERT: A 39 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7824 (mmmt) REVERT: A 80 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7951 (mtpt) REVERT: A 247 ARG cc_start: 0.8915 (mtp85) cc_final: 0.8487 (mtm-85) REVERT: A 258 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 156 LYS cc_start: 0.8839 (mttt) cc_final: 0.8447 (mtpt) REVERT: B 254 ARG cc_start: 0.8767 (ttp80) cc_final: 0.7935 (ttp-110) REVERT: B 285 LYS cc_start: 0.8710 (pttt) cc_final: 0.8450 (ptmm) REVERT: C 110 ASP cc_start: 0.8537 (m-30) cc_final: 0.8259 (m-30) REVERT: C 187 ASP cc_start: 0.8923 (t0) cc_final: 0.8387 (p0) REVERT: C 254 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8089 (ttp-110) REVERT: C 285 LYS cc_start: 0.8733 (pttt) cc_final: 0.8383 (ptmm) outliers start: 11 outliers final: 3 residues processed: 172 average time/residue: 0.1169 time to fit residues: 24.8506 Evaluate side-chains 144 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 185 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.094135 restraints weight = 10830.712| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.28 r_work: 0.2834 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7741 Z= 0.242 Angle : 0.628 7.416 10537 Z= 0.334 Chirality : 0.045 0.140 1197 Planarity : 0.004 0.033 1293 Dihedral : 16.535 151.716 1323 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.43 % Allowed : 17.81 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -2.57 (0.24), residues: 921 helix: -2.18 (0.21), residues: 417 sheet: 1.16 (0.48), residues: 123 loop : -2.01 (0.26), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 130 TYR 0.016 0.002 TYR C 315 PHE 0.019 0.003 PHE B 129 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 7741) covalent geometry : angle 0.62812 (10537) hydrogen bonds : bond 0.04297 ( 248) hydrogen bonds : angle 5.13046 ( 681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.221 Fit side-chains REVERT: A 77 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 247 ARG cc_start: 0.9049 (mtp85) cc_final: 0.8601 (mtm-85) REVERT: B 91 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8130 (tm-30) REVERT: C 110 ASP cc_start: 0.8501 (m-30) cc_final: 0.8225 (m-30) REVERT: C 187 ASP cc_start: 0.9052 (t0) cc_final: 0.8400 (p0) REVERT: C 254 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8239 (ttp-110) outliers start: 18 outliers final: 15 residues processed: 152 average time/residue: 0.1069 time to fit residues: 20.4453 Evaluate side-chains 140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 291 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 0.0270 chunk 75 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.099578 restraints weight = 10853.106| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.27 r_work: 0.2871 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7741 Z= 0.106 Angle : 0.483 5.807 10537 Z= 0.262 Chirality : 0.040 0.124 1197 Planarity : 0.003 0.027 1293 Dihedral : 15.788 152.515 1323 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.89 % Allowed : 19.30 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.75 (0.26), residues: 921 helix: -1.18 (0.24), residues: 417 sheet: 0.82 (0.46), residues: 138 loop : -1.81 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.008 0.001 TYR A 205 PHE 0.010 0.001 PHE B 129 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7741) covalent geometry : angle 0.48315 (10537) hydrogen bonds : bond 0.02585 ( 248) hydrogen bonds : angle 4.51175 ( 681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.232 Fit side-chains REVERT: A 39 LYS cc_start: 0.8405 (mmtp) cc_final: 0.7884 (mmmt) REVERT: A 176 GLU cc_start: 0.8867 (tt0) cc_final: 0.8329 (mt-10) REVERT: A 247 ARG cc_start: 0.9038 (mtp85) cc_final: 0.8577 (mtm-85) REVERT: B 91 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 156 LYS cc_start: 0.8889 (mttt) cc_final: 0.8360 (mtmt) REVERT: B 161 ASP cc_start: 0.8779 (t0) cc_final: 0.8471 (t0) REVERT: B 311 ILE cc_start: 0.9130 (mt) cc_final: 0.8862 (mm) REVERT: C 158 MET cc_start: 0.8621 (ttp) cc_final: 0.7928 (ttt) REVERT: C 176 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8154 (tm-30) REVERT: C 187 ASP cc_start: 0.9000 (t0) cc_final: 0.8342 (p0) outliers start: 14 outliers final: 8 residues processed: 157 average time/residue: 0.1079 time to fit residues: 21.5655 Evaluate side-chains 150 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 0.0060 chunk 16 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101550 restraints weight = 10701.666| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.27 r_work: 0.2936 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7741 Z= 0.102 Angle : 0.469 5.404 10537 Z= 0.254 Chirality : 0.040 0.128 1197 Planarity : 0.003 0.029 1293 Dihedral : 15.308 154.453 1323 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.89 % Allowed : 19.84 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.27), residues: 921 helix: -0.51 (0.25), residues: 423 sheet: 1.00 (0.47), residues: 138 loop : -1.63 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.008 0.001 TYR A 205 PHE 0.009 0.001 PHE B 129 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7741) covalent geometry : angle 0.46876 (10537) hydrogen bonds : bond 0.02484 ( 248) hydrogen bonds : angle 4.29712 ( 681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.270 Fit side-chains REVERT: A 247 ARG cc_start: 0.9018 (mtp85) cc_final: 0.8507 (mtm-85) REVERT: B 91 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 156 LYS cc_start: 0.8906 (mttt) cc_final: 0.8442 (mtmt) REVERT: B 161 ASP cc_start: 0.8744 (t0) cc_final: 0.8421 (t0) REVERT: B 311 ILE cc_start: 0.9141 (mt) cc_final: 0.8927 (mm) REVERT: C 94 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8629 (tp40) REVERT: C 130 ARG cc_start: 0.7692 (ptt-90) cc_final: 0.6600 (tpt170) REVERT: C 158 MET cc_start: 0.8641 (ttp) cc_final: 0.7960 (ttt) REVERT: C 176 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 187 ASP cc_start: 0.8996 (t0) cc_final: 0.8352 (p0) outliers start: 14 outliers final: 14 residues processed: 170 average time/residue: 0.1000 time to fit residues: 21.8619 Evaluate side-chains 165 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.101192 restraints weight = 10823.301| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.25 r_work: 0.2905 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7741 Z= 0.115 Angle : 0.475 5.511 10537 Z= 0.257 Chirality : 0.040 0.127 1197 Planarity : 0.003 0.027 1293 Dihedral : 15.264 154.980 1323 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.97 % Allowed : 20.11 % Favored : 76.92 % 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: -0.79 (0.27), residues: 921 helix: -0.22 (0.26), residues: 426 sheet: 1.11 (0.47), residues: 138 loop : -1.49 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.007 0.001 TYR B 315 PHE 0.009 0.001 PHE B 129 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7741) covalent geometry : angle 0.47482 (10537) hydrogen bonds : bond 0.02522 ( 248) hydrogen bonds : angle 4.25828 ( 681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.275 Fit side-chains REVERT: A 247 ARG cc_start: 0.9043 (mtp85) cc_final: 0.8527 (mtm-85) REVERT: B 91 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 156 LYS cc_start: 0.8919 (mttt) cc_final: 0.8459 (mtmt) REVERT: B 161 ASP cc_start: 0.8727 (t0) cc_final: 0.8420 (t0) REVERT: B 311 ILE cc_start: 0.9125 (mt) cc_final: 0.8908 (mm) REVERT: C 94 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8660 (tp40) REVERT: C 130 ARG cc_start: 0.7721 (ptt-90) cc_final: 0.6646 (tpt170) REVERT: C 158 MET cc_start: 0.8654 (ttp) cc_final: 0.7958 (ttt) REVERT: C 176 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8243 (tm-30) REVERT: C 187 ASP cc_start: 0.9010 (t0) cc_final: 0.8358 (p0) outliers start: 22 outliers final: 17 residues processed: 166 average time/residue: 0.0988 time to fit residues: 21.3253 Evaluate side-chains 157 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 12 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103452 restraints weight = 10761.831| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.26 r_work: 0.2916 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7741 Z= 0.116 Angle : 0.479 5.521 10537 Z= 0.259 Chirality : 0.040 0.128 1197 Planarity : 0.003 0.026 1293 Dihedral : 15.210 155.768 1323 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.56 % Allowed : 20.51 % Favored : 76.92 % 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: -0.51 (0.28), residues: 921 helix: 0.05 (0.26), residues: 423 sheet: 1.18 (0.47), residues: 138 loop : -1.37 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.007 0.001 TYR A 205 PHE 0.009 0.001 PHE B 129 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7741) covalent geometry : angle 0.47864 (10537) hydrogen bonds : bond 0.02526 ( 248) hydrogen bonds : angle 4.24189 ( 681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.215 Fit side-chains REVERT: A 247 ARG cc_start: 0.9046 (mtp85) cc_final: 0.8547 (mtm-85) REVERT: B 91 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 156 LYS cc_start: 0.8916 (mttt) cc_final: 0.8466 (mtmt) REVERT: B 311 ILE cc_start: 0.9135 (mt) cc_final: 0.8913 (mm) REVERT: C 94 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8654 (tp40) REVERT: C 130 ARG cc_start: 0.7696 (ptt-90) cc_final: 0.6720 (tpt170) REVERT: C 158 MET cc_start: 0.8649 (ttp) cc_final: 0.7956 (ttt) REVERT: C 187 ASP cc_start: 0.8961 (t0) cc_final: 0.8322 (p0) outliers start: 19 outliers final: 17 residues processed: 157 average time/residue: 0.0952 time to fit residues: 19.3745 Evaluate side-chains 153 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105913 restraints weight = 10826.677| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.25 r_work: 0.2910 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7741 Z= 0.093 Angle : 0.454 5.256 10537 Z= 0.245 Chirality : 0.039 0.127 1197 Planarity : 0.003 0.028 1293 Dihedral : 15.014 157.814 1323 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.02 % Allowed : 20.92 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.28), residues: 921 helix: 0.27 (0.27), residues: 423 sheet: 1.19 (0.47), residues: 138 loop : -1.28 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.010 0.001 TYR A 205 PHE 0.007 0.001 PHE B 126 HIS 0.001 0.000 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7741) covalent geometry : angle 0.45360 (10537) hydrogen bonds : bond 0.02146 ( 248) hydrogen bonds : angle 4.06552 ( 681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.287 Fit side-chains REVERT: A 206 GLN cc_start: 0.8966 (mt0) cc_final: 0.8695 (tt0) REVERT: A 247 ARG cc_start: 0.9008 (mtp85) cc_final: 0.8573 (mtm-85) REVERT: B 91 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8131 (tm-30) REVERT: B 156 LYS cc_start: 0.8893 (mttt) cc_final: 0.8441 (mtmt) REVERT: B 311 ILE cc_start: 0.9090 (mt) cc_final: 0.8750 (mm) REVERT: C 23 GLN cc_start: 0.7940 (mp10) cc_final: 0.7511 (mp10) REVERT: C 94 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8659 (tp40) REVERT: C 101 GLN cc_start: 0.8394 (mt0) cc_final: 0.8134 (mt0) REVERT: C 130 ARG cc_start: 0.7413 (ptt-90) cc_final: 0.6661 (tpt170) REVERT: C 158 MET cc_start: 0.8598 (ttp) cc_final: 0.7889 (ttt) REVERT: C 187 ASP cc_start: 0.8934 (t0) cc_final: 0.8279 (p0) outliers start: 15 outliers final: 14 residues processed: 168 average time/residue: 0.0960 time to fit residues: 20.9362 Evaluate side-chains 151 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 63 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN C 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.100281 restraints weight = 10840.557| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.26 r_work: 0.2882 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7741 Z= 0.118 Angle : 0.492 5.549 10537 Z= 0.262 Chirality : 0.040 0.133 1197 Planarity : 0.003 0.049 1293 Dihedral : 15.068 156.586 1323 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.43 % Allowed : 21.73 % Favored : 75.84 % 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: -0.15 (0.28), residues: 921 helix: 0.51 (0.27), residues: 405 sheet: 0.97 (0.55), residues: 108 loop : -0.97 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 27 TYR 0.010 0.001 TYR A 205 PHE 0.008 0.001 PHE B 129 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7741) covalent geometry : angle 0.49196 (10537) hydrogen bonds : bond 0.02491 ( 248) hydrogen bonds : angle 4.15412 ( 681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.278 Fit side-chains REVERT: A 247 ARG cc_start: 0.9038 (mtp85) cc_final: 0.8526 (mtm-85) REVERT: B 91 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 156 LYS cc_start: 0.8944 (mttt) cc_final: 0.8470 (mtmt) REVERT: B 311 ILE cc_start: 0.9091 (mt) cc_final: 0.8758 (mm) REVERT: C 23 GLN cc_start: 0.7896 (mp10) cc_final: 0.7455 (mp10) REVERT: C 94 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8644 (tp40) REVERT: C 130 ARG cc_start: 0.7462 (ptt-90) cc_final: 0.6666 (tpt170) REVERT: C 158 MET cc_start: 0.8659 (ttp) cc_final: 0.7925 (ttt) REVERT: C 193 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7714 (ttt180) outliers start: 18 outliers final: 16 residues processed: 156 average time/residue: 0.0999 time to fit residues: 20.1147 Evaluate side-chains 151 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.128540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.102368 restraints weight = 10876.755| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.25 r_work: 0.2942 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7741 Z= 0.107 Angle : 0.477 5.520 10537 Z= 0.254 Chirality : 0.040 0.130 1197 Planarity : 0.003 0.047 1293 Dihedral : 15.009 157.455 1323 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.02 % Allowed : 22.27 % Favored : 75.71 % 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: -0.06 (0.28), residues: 921 helix: 0.62 (0.27), residues: 405 sheet: 0.97 (0.55), residues: 108 loop : -0.95 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 130 TYR 0.006 0.001 TYR A 216 PHE 0.008 0.001 PHE A 126 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7741) covalent geometry : angle 0.47712 (10537) hydrogen bonds : bond 0.02312 ( 248) hydrogen bonds : angle 4.11081 ( 681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.216 Fit side-chains REVERT: A 29 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7062 (mt-10) REVERT: A 247 ARG cc_start: 0.9042 (mtp85) cc_final: 0.8538 (mtm-85) REVERT: B 91 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 156 LYS cc_start: 0.8923 (mttt) cc_final: 0.8486 (mtmt) REVERT: B 311 ILE cc_start: 0.9125 (mt) cc_final: 0.8791 (mm) REVERT: C 23 GLN cc_start: 0.7917 (mp10) cc_final: 0.7502 (mp10) REVERT: C 94 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8668 (tp40) REVERT: C 130 ARG cc_start: 0.7407 (ptt-90) cc_final: 0.6792 (tpt170) REVERT: C 158 MET cc_start: 0.8652 (ttp) cc_final: 0.7934 (ttt) outliers start: 15 outliers final: 15 residues processed: 152 average time/residue: 0.0935 time to fit residues: 18.8230 Evaluate side-chains 148 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.0670 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102335 restraints weight = 10693.758| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.38 r_work: 0.2943 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7741 Z= 0.097 Angle : 0.466 5.297 10537 Z= 0.248 Chirality : 0.040 0.169 1197 Planarity : 0.003 0.046 1293 Dihedral : 14.915 157.983 1323 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.43 % Allowed : 22.00 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.28), residues: 921 helix: 0.68 (0.28), residues: 405 sheet: 1.06 (0.56), residues: 108 loop : -0.90 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 27 TYR 0.009 0.001 TYR A 205 PHE 0.007 0.001 PHE B 126 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7741) covalent geometry : angle 0.46564 (10537) hydrogen bonds : bond 0.02147 ( 248) hydrogen bonds : angle 4.03401 ( 681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.33 seconds wall clock time: 31 minutes 16.56 seconds (1876.56 seconds total)