Starting phenix.real_space_refine on Fri Sep 11 04:45:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c9a_30310/09_2026/7c9a_30310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9a_30310/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7c9a_30310/09_2026/7c9a_30310.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c9a_30310/09_2026/7c9a_30310.cif" model { file = "/net/cci-nas-00/data/ceres_data/7c9a_30310/09_2026/7c9a_30310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9a_30310/09_2026/7c9a_30310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c9a_30310/09_2026/7c9a_30310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9a_30310/09_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1.45, per 1000 atoms: 0.19 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: 0.59 Conformation dependent library (CDL) restraints added in 441.0 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: 0.86 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: 1.36 Time building geometry restraints manager: 0.82 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: 4366 29.29 - 58.58: 230 58.58 - 87.87: 26 87.87 - 117.16: 1 117.16 - 146.45: 6 Dihedral angle restraints: 4629 sinusoidal: 1974 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 4626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 993 0.063 - 0.126: 183 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: 5.240 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 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= 0.383 Angle : 1.051 20.922 10537 Z= 0.615 Chirality : 0.049 0.314 1197 Planarity : 0.005 0.039 1293 Dihedral : 17.668 146.452 2931 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/Z covalent geometry : bond 0.00725 / 0.38 ( 7741) covalent geometry : angle 1.05059 / 0.61 (10537) hydrogen bonds : bond 0.33272 / 22.05 ( 248) hydrogen bonds : angle 10.49934 / 7.04 ( 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 : 0.278 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: 0.1350 time to fit residues: 38.0810 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 : 0.260 ------------------------------------------------------------------------------- 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... A 242 GLN B 34 ASN B 242 GLN C 242 GLN ** C 290 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 = 0.3351 r_free = 0.3351 target = 0.126258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.100422 restraints weight = 10830.891| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.22 r_work: 0.2982 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7741 Z= 0.189 Angle : 0.652 8.741 10537 Z= 0.364 Chirality : 0.045 0.183 1197 Planarity : 0.005 0.037 1293 Dihedral : 16.123 156.619 1239 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 2.83 % Allowed : 11.74 % Favored : 85.43 % 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: -3.78 (0.22), residues: 921 helix: -3.52 (0.15), residues: 411 sheet: 0.91 (0.48), residues: 120 loop : -2.32 (0.24), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 299 TYR 0.010 0.002 TYR C 315 PHE 0.014 0.002 PHE C 166 HIS 0.004 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 7741) covalent geometry : angle 0.65228 / 0.36 (10537) hydrogen bonds : bond 0.05407 / 3.57 ( 248) hydrogen bonds : angle 5.87799 / 4.03 ( 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: 21 poor density : 157 time to evaluate : 0.263 Fit side-chains REVERT: A 39 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7924 (mmmt) REVERT: A 247 ARG cc_start: 0.8857 (mtp85) cc_final: 0.8474 (mtm-85) REVERT: A 258 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8265 (mt-10) REVERT: B 66 ILE cc_start: 0.7796 (mm) cc_final: 0.7516 (mm) REVERT: B 156 LYS cc_start: 0.8882 (mttt) cc_final: 0.8393 (mtpt) REVERT: B 254 ARG cc_start: 0.8737 (ttp80) cc_final: 0.7936 (ttp-110) REVERT: C 94 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8608 (tp40) REVERT: C 110 ASP cc_start: 0.8481 (m-30) cc_final: 0.8236 (m-30) REVERT: C 187 ASP cc_start: 0.8849 (t0) cc_final: 0.8366 (p0) REVERT: C 285 LYS cc_start: 0.8826 (pttt) cc_final: 0.8473 (ptmm) outliers start: 21 outliers final: 11 residues processed: 167 average time/residue: 0.1096 time to fit residues: 23.2636 Evaluate side-chains 155 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 223 SER 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: 2.9990 chunk 83 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 81 optimal weight: 0.0170 chunk 65 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN C 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.124597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.097989 restraints weight = 10742.961| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.27 r_work: 0.2853 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7741 Z= 0.182 Angle : 0.587 7.614 10537 Z= 0.325 Chirality : 0.044 0.153 1197 Planarity : 0.004 0.030 1293 Dihedral : 16.045 158.692 1239 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.16 % Allowed : 14.98 % Favored : 82.86 % 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: -2.53 (0.24), residues: 921 helix: -2.11 (0.21), residues: 411 sheet: 1.21 (0.48), residues: 120 loop : -2.04 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 130 TYR 0.011 0.001 TYR C 315 PHE 0.015 0.002 PHE A 129 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 7741) covalent geometry : angle 0.58691 / 0.32 (10537) hydrogen bonds : bond 0.04261 / 2.85 ( 248) hydrogen bonds : angle 5.13956 / 3.55 ( 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 164 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.256 Fit side-chains REVERT: A 39 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7872 (mmmt) REVERT: A 77 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 247 ARG cc_start: 0.9034 (mtp85) cc_final: 0.8555 (mtm-85) REVERT: A 258 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8159 (mt-10) REVERT: B 156 LYS cc_start: 0.8851 (mttt) cc_final: 0.8405 (mtpt) REVERT: B 254 ARG cc_start: 0.8782 (ttp80) cc_final: 0.7908 (ttp-110) REVERT: C 110 ASP cc_start: 0.8468 (m-30) cc_final: 0.8236 (m-30) REVERT: C 187 ASP cc_start: 0.8942 (t0) cc_final: 0.8437 (p0) REVERT: C 254 ARG cc_start: 0.8501 (mtm110) cc_final: 0.8171 (ttp-110) REVERT: C 285 LYS cc_start: 0.8713 (pttt) cc_final: 0.8354 (ptmm) outliers start: 16 outliers final: 13 residues processed: 156 average time/residue: 0.1067 time to fit residues: 21.0233 Evaluate side-chains 141 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 60 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.098452 restraints weight = 10902.175| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.25 r_work: 0.2867 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7741 Z= 0.145 Angle : 0.549 6.580 10537 Z= 0.300 Chirality : 0.043 0.198 1197 Planarity : 0.004 0.033 1293 Dihedral : 15.941 165.059 1239 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.97 % Allowed : 16.06 % Favored : 80.97 % 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: -1.77 (0.26), residues: 921 helix: -1.22 (0.24), residues: 411 sheet: 1.47 (0.49), residues: 120 loop : -1.93 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 167 TYR 0.009 0.001 TYR B 315 PHE 0.011 0.002 PHE B 129 HIS 0.003 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 7741) covalent geometry : angle 0.54880 / 0.30 (10537) hydrogen bonds : bond 0.03289 / 2.21 ( 248) hydrogen bonds : angle 4.81353 / 3.34 ( 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 173 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.275 Fit side-chains REVERT: A 39 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7940 (mmmt) REVERT: A 247 ARG cc_start: 0.9085 (mtp85) cc_final: 0.8651 (mtm-85) REVERT: B 91 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 156 LYS cc_start: 0.8917 (mttt) cc_final: 0.8438 (mtmt) REVERT: B 254 ARG cc_start: 0.8840 (ttp80) cc_final: 0.7961 (ttp-110) REVERT: C 110 ASP cc_start: 0.8445 (m-30) cc_final: 0.8233 (m-30) REVERT: C 187 ASP cc_start: 0.8967 (t0) cc_final: 0.8432 (p0) REVERT: C 285 LYS cc_start: 0.8671 (pttt) cc_final: 0.8337 (ptmm) outliers start: 22 outliers final: 16 residues processed: 164 average time/residue: 0.1019 time to fit residues: 21.6956 Evaluate side-chains 157 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 131 THR 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 216 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.124182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.097618 restraints weight = 10802.426| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.28 r_work: 0.2850 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7741 Z= 0.158 Angle : 0.537 6.531 10537 Z= 0.296 Chirality : 0.043 0.171 1197 Planarity : 0.003 0.032 1293 Dihedral : 15.935 168.358 1239 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.83 % Allowed : 18.08 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -1.31 (0.27), residues: 921 helix: -0.73 (0.25), residues: 414 sheet: 1.70 (0.51), residues: 120 loop : -1.83 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.009 0.001 TYR C 315 PHE 0.011 0.002 PHE B 129 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 7741) covalent geometry : angle 0.53727 / 0.30 (10537) hydrogen bonds : bond 0.03276 / 2.20 ( 248) hydrogen bonds : angle 4.71483 / 3.26 ( 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 159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.279 Fit side-chains REVERT: A 247 ARG cc_start: 0.9088 (mtp85) cc_final: 0.8621 (mtm-85) REVERT: B 91 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 156 LYS cc_start: 0.8955 (mttt) cc_final: 0.8450 (mtmt) REVERT: B 231 ASP cc_start: 0.8542 (m-30) cc_final: 0.8305 (m-30) REVERT: B 254 ARG cc_start: 0.8810 (ttp80) cc_final: 0.7911 (ttp-110) REVERT: C 110 ASP cc_start: 0.8479 (m-30) cc_final: 0.8268 (m-30) REVERT: C 130 ARG cc_start: 0.7841 (ptt-90) cc_final: 0.6386 (tpt170) REVERT: C 187 ASP cc_start: 0.8954 (t0) cc_final: 0.8380 (p0) REVERT: C 285 LYS cc_start: 0.8635 (pttt) cc_final: 0.8418 (ptmm) outliers start: 21 outliers final: 20 residues processed: 149 average time/residue: 0.1077 time to fit residues: 20.3244 Evaluate side-chains 154 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.099537 restraints weight = 10859.010| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.31 r_work: 0.2897 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3398 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= 0.108 Angle : 0.495 5.868 10537 Z= 0.274 Chirality : 0.041 0.154 1197 Planarity : 0.003 0.033 1293 Dihedral : 15.809 173.400 1239 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.70 % Allowed : 19.30 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.96 (0.28), residues: 921 helix: -0.28 (0.26), residues: 420 sheet: 1.06 (0.49), residues: 138 loop : -1.69 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.008 0.001 TYR B 205 PHE 0.008 0.001 PHE B 129 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 7741) covalent geometry : angle 0.49454 / 0.27 (10537) hydrogen bonds : bond 0.02669 / 1.78 ( 248) hydrogen bonds : angle 4.48255 / 3.11 ( 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 178 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.269 Fit side-chains REVERT: A 176 GLU cc_start: 0.8867 (tt0) cc_final: 0.8328 (mt-10) REVERT: A 205 TYR cc_start: 0.8632 (m-10) cc_final: 0.8239 (m-10) REVERT: A 247 ARG cc_start: 0.9054 (mtp85) cc_final: 0.8612 (mtm-85) REVERT: B 91 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 156 LYS cc_start: 0.8925 (mttt) cc_final: 0.8443 (mtmt) REVERT: B 254 ARG cc_start: 0.8820 (ttp80) cc_final: 0.7923 (ttp-110) REVERT: C 94 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8530 (tp40) REVERT: C 130 ARG cc_start: 0.7777 (ptt-90) cc_final: 0.6475 (tpt170) REVERT: C 176 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 187 ASP cc_start: 0.8971 (t0) cc_final: 0.8346 (p0) REVERT: C 254 ARG cc_start: 0.8494 (mtm110) cc_final: 0.8228 (ttp-110) REVERT: C 285 LYS cc_start: 0.8641 (pttt) cc_final: 0.8392 (ptmm) outliers start: 20 outliers final: 16 residues processed: 167 average time/residue: 0.0994 time to fit residues: 21.4350 Evaluate side-chains 165 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 326 MET 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 174 VAL Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.100025 restraints weight = 10771.165| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.27 r_work: 0.2901 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7741 Z= 0.103 Angle : 0.483 5.664 10537 Z= 0.267 Chirality : 0.041 0.153 1197 Planarity : 0.003 0.032 1293 Dihedral : 15.699 177.211 1239 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.97 % Allowed : 19.03 % Favored : 78.00 % 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: -0.66 (0.28), residues: 921 helix: 0.08 (0.27), residues: 417 sheet: 1.05 (0.49), residues: 138 loop : -1.60 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.005 0.001 TYR C 159 PHE 0.008 0.001 PHE B 129 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 7741) covalent geometry : angle 0.48259 / 0.27 (10537) hydrogen bonds : bond 0.02480 / 1.65 ( 248) hydrogen bonds : angle 4.34077 / 3.02 ( 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 177 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.290 Fit side-chains REVERT: A 176 GLU cc_start: 0.8824 (tt0) cc_final: 0.8299 (mt-10) REVERT: A 205 TYR cc_start: 0.8623 (m-10) cc_final: 0.8181 (m-10) REVERT: A 247 ARG cc_start: 0.9043 (mtp85) cc_final: 0.8612 (mtm-85) REVERT: B 91 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8003 (tm-30) REVERT: B 156 LYS cc_start: 0.8922 (mttt) cc_final: 0.8444 (mtmt) REVERT: B 254 ARG cc_start: 0.8830 (ttp80) cc_final: 0.7927 (ttp-110) REVERT: C 94 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8575 (tp40) REVERT: C 130 ARG cc_start: 0.7706 (ptt-90) cc_final: 0.6570 (tpt170) REVERT: C 176 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8047 (tm-30) REVERT: C 187 ASP cc_start: 0.8971 (t0) cc_final: 0.8342 (p0) REVERT: C 254 ARG cc_start: 0.8472 (mtm110) cc_final: 0.8182 (ttp-110) REVERT: C 285 LYS cc_start: 0.8626 (pttt) cc_final: 0.8391 (ptmm) outliers start: 22 outliers final: 17 residues processed: 165 average time/residue: 0.0968 time to fit residues: 20.8559 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 : 0.223 ------------------------------------------------------------------------------- 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 326 MET 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 158 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.101896 restraints weight = 10877.544| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.28 r_work: 0.2940 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3654 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= 0.110 Angle : 0.489 5.552 10537 Z= 0.270 Chirality : 0.041 0.155 1197 Planarity : 0.003 0.032 1293 Dihedral : 15.624 179.068 1239 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.56 % Allowed : 19.84 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.28), residues: 921 helix: 0.13 (0.27), residues: 429 sheet: 1.04 (0.49), residues: 138 loop : -1.51 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.006 0.001 TYR C 315 PHE 0.009 0.001 PHE B 129 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7741) covalent geometry : angle 0.48906 / 0.27 (10537) hydrogen bonds : bond 0.02461 / 1.63 ( 248) hydrogen bonds : angle 4.26834 / 2.96 ( 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 157 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.202 Fit side-chains REVERT: A 176 GLU cc_start: 0.8804 (tt0) cc_final: 0.8281 (mt-10) REVERT: A 205 TYR cc_start: 0.8604 (m-10) cc_final: 0.8238 (m-10) REVERT: A 247 ARG cc_start: 0.9057 (mtp85) cc_final: 0.8632 (mtm-85) REVERT: A 332 ASP cc_start: 0.8514 (m-30) cc_final: 0.8188 (p0) REVERT: B 91 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 156 LYS cc_start: 0.8939 (mttt) cc_final: 0.8478 (mtmt) REVERT: C 94 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8572 (tp40) REVERT: C 130 ARG cc_start: 0.7741 (ptt-90) cc_final: 0.6652 (tpt170) REVERT: C 176 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 187 ASP cc_start: 0.8973 (t0) cc_final: 0.8351 (p0) REVERT: C 254 ARG cc_start: 0.8486 (mtm110) cc_final: 0.8210 (ttp-110) REVERT: C 285 LYS cc_start: 0.8653 (pttt) cc_final: 0.8248 (ptmm) outliers start: 19 outliers final: 15 residues processed: 150 average time/residue: 0.0948 time to fit residues: 18.5032 Evaluate side-chains 150 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 326 MET 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 174 VAL 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 163 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 33 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.107240 restraints weight = 10700.629| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.27 r_work: 0.2884 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7741 Z= 0.120 Angle : 0.490 5.683 10537 Z= 0.269 Chirality : 0.041 0.159 1197 Planarity : 0.003 0.031 1293 Dihedral : 15.562 174.957 1239 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.56 % Allowed : 19.97 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.28), residues: 921 helix: 0.23 (0.27), residues: 429 sheet: 1.00 (0.49), residues: 138 loop : -1.44 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.007 0.001 TYR B 315 PHE 0.008 0.001 PHE A 126 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7741) covalent geometry : angle 0.48969 / 0.27 (10537) hydrogen bonds : bond 0.02551 / 1.70 ( 248) hydrogen bonds : angle 4.25626 / 2.95 ( 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 163 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.276 Fit side-chains REVERT: A 176 GLU cc_start: 0.8848 (tt0) cc_final: 0.8344 (mt-10) REVERT: A 205 TYR cc_start: 0.8628 (m-10) cc_final: 0.8365 (m-10) REVERT: A 247 ARG cc_start: 0.9026 (mtp85) cc_final: 0.8603 (mtm-85) REVERT: A 332 ASP cc_start: 0.8524 (m-30) cc_final: 0.8162 (p0) REVERT: B 91 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8095 (tm-30) REVERT: B 156 LYS cc_start: 0.8943 (mttt) cc_final: 0.8459 (mtmt) REVERT: B 311 ILE cc_start: 0.9113 (mt) cc_final: 0.8787 (mm) REVERT: C 94 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8566 (tp40) REVERT: C 130 ARG cc_start: 0.7689 (ptt-90) cc_final: 0.6634 (tpt170) REVERT: C 176 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 187 ASP cc_start: 0.8915 (t0) cc_final: 0.8302 (p0) REVERT: C 285 LYS cc_start: 0.8613 (pttt) cc_final: 0.8216 (ptmm) outliers start: 19 outliers final: 16 residues processed: 154 average time/residue: 0.0877 time to fit residues: 17.5573 Evaluate side-chains 154 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR 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: 5.9990 chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.094940 restraints weight = 11068.003| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.27 r_work: 0.2781 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 7741 Z= 0.304 Angle : 0.674 7.979 10537 Z= 0.357 Chirality : 0.049 0.222 1197 Planarity : 0.005 0.057 1293 Dihedral : 15.798 173.092 1239 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.10 % Allowed : 19.30 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.75 (0.28), residues: 921 helix: -0.10 (0.26), residues: 426 sheet: 1.02 (0.49), residues: 135 loop : -1.51 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 254 TYR 0.016 0.002 TYR C 315 PHE 0.020 0.003 PHE B 327 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.30 ( 7741) covalent geometry : angle 0.67405 / 0.36 (10537) hydrogen bonds : bond 0.04162 / 2.76 ( 248) hydrogen bonds : angle 4.79192 / 3.32 ( 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 147 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.446 Fit side-chains REVERT: A 247 ARG cc_start: 0.9075 (mtp85) cc_final: 0.8576 (mtm-85) REVERT: A 332 ASP cc_start: 0.8604 (m-30) cc_final: 0.8166 (p0) REVERT: B 91 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 156 LYS cc_start: 0.9050 (mttt) cc_final: 0.8526 (mtmt) REVERT: C 130 ARG cc_start: 0.7899 (ptt-90) cc_final: 0.6531 (tpt170) REVERT: C 176 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 285 LYS cc_start: 0.8640 (pttt) cc_final: 0.8403 (ptmm) outliers start: 23 outliers final: 19 residues processed: 138 average time/residue: 0.1162 time to fit residues: 20.6312 Evaluate side-chains 140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 GLU 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 129 PHE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 181 SER 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 66 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 174 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.0030 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 65 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.125074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098539 restraints weight = 10798.783| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.28 r_work: 0.2897 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7741 Z= 0.114 Angle : 0.525 8.694 10537 Z= 0.286 Chirality : 0.042 0.164 1197 Planarity : 0.003 0.033 1293 Dihedral : 15.602 168.430 1239 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.16 % Allowed : 20.65 % Favored : 77.19 % 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: -0.44 (0.28), residues: 921 helix: 0.25 (0.27), residues: 420 sheet: 1.05 (0.50), residues: 135 loop : -1.42 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.007 0.001 TYR A 232 PHE 0.010 0.001 PHE B 129 HIS 0.002 0.000 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 7741) covalent geometry : angle 0.52546 / 0.29 (10537) hydrogen bonds : bond 0.02752 / 1.84 ( 248) hydrogen bonds : angle 4.42346 / 3.07 ( 681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.98 seconds wall clock time: 34 minutes 5.80 seconds (2045.80 seconds total)