Starting phenix.real_space_refine on Sat Sep 12 09:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m66_30114/09_2026/6m66_30114.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m66_30114/09_2026/6m66_30114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m66_30114/09_2026/6m66_30114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m66_30114/09_2026/6m66_30114.map" model { file = "/net/cci-nas-00/data/ceres_data/6m66_30114/09_2026/6m66_30114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m66_30114/09_2026/6m66_30114.cif" } resolution = 4.1 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= 0.015 sd= 0.098 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9975 2.51 5 N 2303 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s 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: 14938 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.20, per 1000 atoms: 0.15 Number of scatterers: 14938 At special positions: 0 Unit cell: (113.94, 113.94, 113.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2590 8.00 N 2303 7.00 C 9975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.02 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.02 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.02 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.02 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.02 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.02 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 464.9 milliseconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 72.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 removed outlier: 5.032A pdb=" N ILE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.698A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.595A pdb=" N HIS A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 131 removed outlier: 4.106A pdb=" N LEU A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 157 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'B' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.698A pdb=" N GLN B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 157 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU B 310 " --> pdb=" O LYS B 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 310' Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'C' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.698A pdb=" N GLN C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.595A pdb=" N HIS C 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 157 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C 220 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU C 310 " --> pdb=" O LYS C 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 310' Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.749A pdb=" N ASP C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'D' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.698A pdb=" N GLN D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 157 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 220 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 234 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 removed outlier: 4.443A pdb=" N GLU D 310 " --> pdb=" O LYS D 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 310' Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.749A pdb=" N ASP D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL D 317 " --> pdb=" O PRO D 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'E' and resid 36 through 59 removed outlier: 5.031A pdb=" N ILE E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.697A pdb=" N GLN E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 157 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 220 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY E 232 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU E 310 " --> pdb=" O LYS E 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 307 through 310' Processing helix chain 'E' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL E 317 " --> pdb=" O PRO E 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 336 Processing helix chain 'F' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.697A pdb=" N GLN F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU F 115 " --> pdb=" O TYR F 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 157 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 198 through 203 Processing helix chain 'F' and resid 209 through 238 removed outlier: 3.771A pdb=" N TYR F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 220 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY F 232 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR F 234 " --> pdb=" O TYR F 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN F 255 " --> pdb=" O GLY F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU F 310 " --> pdb=" O LYS F 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 310' Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL F 317 " --> pdb=" O PRO F 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 336 Processing helix chain 'G' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE G 41 " --> pdb=" O MET G 37 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.697A pdb=" N GLN G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 removed outlier: 4.106A pdb=" N LEU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 157 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR G 220 " --> pdb=" O CYS G 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY G 232 " --> pdb=" O CYS G 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 256 removed outlier: 4.138A pdb=" N ASN G 255 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 295 removed outlier: 4.120A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU G 310 " --> pdb=" O LYS G 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 307 through 310' Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL G 317 " --> pdb=" O PRO G 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS G 319 " --> pdb=" O PHE G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 336 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS A 266 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS B 266 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.910A pdb=" N LYS C 266 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS D 266 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.910A pdb=" N LYS E 266 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS F 266 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS G 266 " --> pdb=" O SER G 65 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4322 1.34 - 1.46: 3089 1.46 - 1.57: 7814 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15309 Sorted by residual: bond pdb=" C VAL C 297 " pdb=" N PRO C 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.95e+00 bond pdb=" C VAL A 297 " pdb=" N PRO A 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.83e+00 bond pdb=" C VAL G 297 " pdb=" N PRO G 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.82e+00 bond pdb=" C VAL E 297 " pdb=" N PRO E 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.80e+00 bond pdb=" C VAL D 297 " pdb=" N PRO D 298 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.75e+00 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 19352 1.74 - 3.47: 1098 3.47 - 5.21: 222 5.21 - 6.95: 91 6.95 - 8.68: 62 Bond angle restraints: 20825 Sorted by residual: angle pdb=" N LEU B 122 " pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 109.81 117.99 -8.18 2.21e+00 2.05e-01 1.37e+01 angle pdb=" N LEU G 122 " pdb=" CA LEU G 122 " pdb=" C LEU G 122 " ideal model delta sigma weight residual 109.81 117.98 -8.17 2.21e+00 2.05e-01 1.37e+01 angle pdb=" N LEU D 122 " pdb=" CA LEU D 122 " pdb=" C LEU D 122 " ideal model delta sigma weight residual 109.81 117.97 -8.16 2.21e+00 2.05e-01 1.36e+01 angle pdb=" N LEU F 122 " pdb=" CA LEU F 122 " pdb=" C LEU F 122 " ideal model delta sigma weight residual 109.81 117.96 -8.15 2.21e+00 2.05e-01 1.36e+01 angle pdb=" N LEU A 122 " pdb=" CA LEU A 122 " pdb=" C LEU A 122 " ideal model delta sigma weight residual 109.81 117.95 -8.14 2.21e+00 2.05e-01 1.36e+01 ... (remaining 20820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.27: 7305 14.27 - 28.53: 1291 28.53 - 42.80: 420 42.80 - 57.07: 84 57.07 - 71.33: 14 Dihedral angle restraints: 9114 sinusoidal: 3563 harmonic: 5551 Sorted by residual: dihedral pdb=" CA PRO C 260 " pdb=" C PRO C 260 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO A 260 " pdb=" C PRO A 260 " pdb=" N ASP A 261 " pdb=" CA ASP A 261 " ideal model delta harmonic sigma weight residual 180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO D 260 " pdb=" C PRO D 260 " pdb=" N ASP D 261 " pdb=" CA ASP D 261 " ideal model delta harmonic sigma weight residual -180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 9111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1431 0.045 - 0.091: 758 0.091 - 0.136: 183 0.136 - 0.181: 85 0.181 - 0.226: 14 Chirality restraints: 2471 Sorted by residual: chirality pdb=" CA PHE C 109 " pdb=" N PHE C 109 " pdb=" C PHE C 109 " pdb=" CB PHE C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE A 109 " pdb=" N PHE A 109 " pdb=" C PHE A 109 " pdb=" CB PHE A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PHE F 109 " pdb=" N PHE F 109 " pdb=" C PHE F 109 " pdb=" CB PHE F 109 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2468 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 123 " -0.054 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 124 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " 0.054 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO G 124 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " -0.054 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO C 124 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " -0.045 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2999 2.76 - 3.30: 14723 3.30 - 3.83: 25889 3.83 - 4.37: 28545 4.37 - 4.90: 46095 Nonbonded interactions: 118251 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 275 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 275 " model vdw 2.257 3.040 nonbonded pdb=" O ARG G 217 " pdb=" OG1 THR G 220 " model vdw 2.279 3.040 nonbonded pdb=" O ARG C 217 " pdb=" OG1 THR C 220 " model vdw 2.280 3.040 nonbonded pdb=" O ARG F 217 " pdb=" OG1 THR F 220 " model vdw 2.280 3.040 ... (remaining 118246 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue 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: 1.190 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.660 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.005 0.054 15323 Z= 0.263 Angle : 1.076 8.681 20853 Z= 0.566 Chirality : 0.060 0.226 2471 Planarity : 0.010 0.080 2520 Dihedral : 16.352 71.333 5460 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % 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: -5.00 (0.14), residues: 1827 helix: -3.08 (0.11), residues: 1008 sheet: -4.52 (0.40), residues: 70 loop : -3.38 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 254 TYR 0.017 0.002 TYR F 309 PHE 0.028 0.002 PHE E 109 TRP 0.008 0.002 TRP E 127 HIS 0.004 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.26 (15309) covalent geometry : angle 1.07623 / 0.57 (20825) SS BOND : bond 0.00522 / 0.31 ( 14) SS BOND : angle 1.14911 / 0.72 ( 28) hydrogen bonds : bond 0.22734 / 14.57 ( 736) hydrogen bonds : angle 8.24486 / 5.63 ( 2187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 VAL cc_start: 0.9217 (t) cc_final: 0.8970 (p) REVERT: A 144 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9186 (tm-30) REVERT: B 38 VAL cc_start: 0.9216 (t) cc_final: 0.8999 (p) REVERT: B 128 ARG cc_start: 0.9427 (tmm-80) cc_final: 0.9216 (ttp-110) REVERT: B 141 PHE cc_start: 0.7595 (m-10) cc_final: 0.7358 (m-80) REVERT: B 144 GLU cc_start: 0.9464 (tm-30) cc_final: 0.9194 (tm-30) REVERT: C 141 PHE cc_start: 0.7614 (m-10) cc_final: 0.7411 (m-80) REVERT: C 144 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9219 (tm-30) REVERT: C 152 ARG cc_start: 0.5779 (ttt180) cc_final: 0.5517 (ptt90) REVERT: D 128 ARG cc_start: 0.9498 (tmm-80) cc_final: 0.9250 (ttp-110) REVERT: D 141 PHE cc_start: 0.7765 (m-10) cc_final: 0.7422 (m-80) REVERT: D 144 GLU cc_start: 0.9451 (tm-30) cc_final: 0.9154 (tm-30) REVERT: D 152 ARG cc_start: 0.5509 (ttt180) cc_final: 0.5176 (ptt90) REVERT: E 128 ARG cc_start: 0.9452 (tmm-80) cc_final: 0.9141 (ttp-110) REVERT: F 38 VAL cc_start: 0.9311 (t) cc_final: 0.9097 (p) REVERT: F 152 ARG cc_start: 0.5709 (ttt180) cc_final: 0.5467 (ptt90) REVERT: G 38 VAL cc_start: 0.9324 (t) cc_final: 0.9100 (p) REVERT: G 144 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9180 (tm-30) REVERT: G 152 ARG cc_start: 0.5803 (ttt180) cc_final: 0.5523 (ptt90) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1299 time to fit residues: 46.5279 Evaluate side-chains 130 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 HIS A 319 HIS A 332 ASN B 134 HIS B 319 HIS C 134 HIS C 319 HIS C 332 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 319 HIS E 134 HIS E 319 HIS F 134 HIS F 319 HIS G 134 HIS G 319 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.095241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074176 restraints weight = 67940.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.075830 restraints weight = 43271.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.077029 restraints weight = 32043.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077733 restraints weight = 26230.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.078089 restraints weight = 23187.660| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15323 Z= 0.176 Angle : 0.852 9.151 20853 Z= 0.417 Chirality : 0.050 0.218 2471 Planarity : 0.007 0.053 2520 Dihedral : 6.576 22.427 1981 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % 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: -3.52 (0.17), residues: 1827 helix: -1.65 (0.13), residues: 1134 sheet: -4.87 (0.36), residues: 84 loop : -3.04 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 128 TYR 0.030 0.002 TYR E 234 PHE 0.020 0.001 PHE E 141 TRP 0.010 0.002 TRP B 127 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (15309) covalent geometry : angle 0.85095 / 0.42 (20825) SS BOND : bond 0.00405 / 0.24 ( 14) SS BOND : angle 1.35767 / 0.79 ( 28) hydrogen bonds : bond 0.05242 / 3.31 ( 736) hydrogen bonds : angle 5.63975 / 3.83 ( 2187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7977 (mm110) cc_final: 0.7687 (mm110) REVERT: A 128 ARG cc_start: 0.9395 (ttp-110) cc_final: 0.9180 (ttp80) REVERT: A 141 PHE cc_start: 0.7741 (m-10) cc_final: 0.7533 (m-80) REVERT: A 272 ILE cc_start: 0.9326 (pt) cc_final: 0.9020 (tt) REVERT: B 56 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7624 (mm110) REVERT: B 128 ARG cc_start: 0.9563 (tmm-80) cc_final: 0.9276 (ttp-110) REVERT: B 272 ILE cc_start: 0.9221 (pt) cc_final: 0.8910 (tt) REVERT: C 36 LYS cc_start: 0.8710 (tmmt) cc_final: 0.8488 (tptt) REVERT: C 141 PHE cc_start: 0.7640 (m-10) cc_final: 0.7438 (m-80) REVERT: C 152 ARG cc_start: 0.5893 (ttt180) cc_final: 0.5579 (ptt90) REVERT: D 128 ARG cc_start: 0.9508 (tmm-80) cc_final: 0.9292 (ttp-110) REVERT: D 141 PHE cc_start: 0.7693 (m-10) cc_final: 0.7415 (m-80) REVERT: D 152 ARG cc_start: 0.5398 (ttt180) cc_final: 0.5111 (ptt90) REVERT: E 56 GLN cc_start: 0.7885 (mm110) cc_final: 0.7543 (mm110) REVERT: E 128 ARG cc_start: 0.9493 (tmm-80) cc_final: 0.9156 (ttp-110) REVERT: E 272 ILE cc_start: 0.9297 (pt) cc_final: 0.9053 (tt) REVERT: F 141 PHE cc_start: 0.7812 (m-10) cc_final: 0.7580 (m-80) REVERT: F 152 ARG cc_start: 0.5664 (ttt180) cc_final: 0.5422 (ptt90) REVERT: G 128 ARG cc_start: 0.9418 (ttp-110) cc_final: 0.9208 (ttp80) REVERT: G 141 PHE cc_start: 0.7672 (m-10) cc_final: 0.7439 (m-80) REVERT: G 152 ARG cc_start: 0.5717 (ttt180) cc_final: 0.5471 (ptt90) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1412 time to fit residues: 37.1671 Evaluate side-chains 109 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 135 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 0.0170 chunk 116 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN E 207 ASN F 332 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.096377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.076219 restraints weight = 66275.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.077369 restraints weight = 43591.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.078168 restraints weight = 32328.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.078452 restraints weight = 28939.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.078529 restraints weight = 26539.659| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15323 Z= 0.142 Angle : 0.785 9.191 20853 Z= 0.380 Chirality : 0.048 0.188 2471 Planarity : 0.007 0.053 2520 Dihedral : 6.025 21.149 1981 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % 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: -2.87 (0.18), residues: 1827 helix: -1.08 (0.14), residues: 1134 sheet: -4.09 (0.48), residues: 84 loop : -3.00 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 128 TYR 0.019 0.001 TYR E 234 PHE 0.021 0.001 PHE B 141 TRP 0.011 0.001 TRP G 127 HIS 0.001 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (15309) covalent geometry : angle 0.78451 / 0.38 (20825) SS BOND : bond 0.00223 / 0.13 ( 14) SS BOND : angle 1.11114 / 0.63 ( 28) hydrogen bonds : bond 0.04522 / 2.91 ( 736) hydrogen bonds : angle 5.10343 / 3.46 ( 2187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9425 (ttp-110) cc_final: 0.9193 (ttp-110) REVERT: A 141 PHE cc_start: 0.7699 (m-10) cc_final: 0.7411 (m-80) REVERT: B 128 ARG cc_start: 0.9607 (tmm-80) cc_final: 0.9322 (ttp-110) REVERT: C 36 LYS cc_start: 0.8928 (tmmt) cc_final: 0.8678 (tptt) REVERT: C 56 GLN cc_start: 0.8081 (mm110) cc_final: 0.7201 (mm-40) REVERT: D 141 PHE cc_start: 0.7704 (m-10) cc_final: 0.7406 (m-80) REVERT: D 152 ARG cc_start: 0.5367 (ttt180) cc_final: 0.5068 (ptt90) REVERT: E 56 GLN cc_start: 0.8048 (mm110) cc_final: 0.7679 (mm110) REVERT: E 128 ARG cc_start: 0.9576 (tmm-80) cc_final: 0.9237 (ttp-110) REVERT: F 56 GLN cc_start: 0.8111 (mt0) cc_final: 0.7829 (mm110) REVERT: F 141 PHE cc_start: 0.7770 (m-10) cc_final: 0.7557 (m-80) REVERT: F 272 ILE cc_start: 0.9315 (pt) cc_final: 0.8998 (tt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1347 time to fit residues: 32.8893 Evaluate side-chains 115 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 112 optimal weight: 0.3980 chunk 169 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 166 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.1668 > 50:) overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.096116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074495 restraints weight = 65343.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.076131 restraints weight = 42116.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.077211 restraints weight = 31612.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077962 restraints weight = 26511.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.078379 restraints weight = 23701.842| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15323 Z= 0.155 Angle : 0.782 9.100 20853 Z= 0.378 Chirality : 0.048 0.191 2471 Planarity : 0.006 0.056 2520 Dihedral : 5.849 19.664 1981 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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: -2.41 (0.18), residues: 1827 helix: -0.67 (0.14), residues: 1162 sheet: -4.32 (0.53), residues: 84 loop : -2.93 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.029 0.001 TYR B 234 PHE 0.025 0.001 PHE G 141 TRP 0.014 0.001 TRP A 127 HIS 0.001 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15309) covalent geometry : angle 0.78098 / 0.38 (20825) SS BOND : bond 0.00778 / 0.50 ( 14) SS BOND : angle 1.38333 / 0.86 ( 28) hydrogen bonds : bond 0.03985 / 2.57 ( 736) hydrogen bonds : angle 4.94900 / 3.35 ( 2187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8067 (mm110) cc_final: 0.7302 (mm-40) REVERT: A 128 ARG cc_start: 0.9413 (ttp-110) cc_final: 0.9183 (ttp-110) REVERT: A 217 ARG cc_start: 0.9190 (mtm180) cc_final: 0.8590 (mtp-110) REVERT: A 272 ILE cc_start: 0.9313 (pt) cc_final: 0.9009 (pt) REVERT: B 56 GLN cc_start: 0.7974 (mm110) cc_final: 0.7235 (mm-40) REVERT: B 272 ILE cc_start: 0.9269 (pt) cc_final: 0.8970 (pt) REVERT: C 56 GLN cc_start: 0.8127 (mm110) cc_final: 0.7189 (mm-40) REVERT: D 56 GLN cc_start: 0.8081 (mm110) cc_final: 0.7421 (mm-40) REVERT: D 141 PHE cc_start: 0.7713 (m-10) cc_final: 0.7427 (m-80) REVERT: D 152 ARG cc_start: 0.5358 (ttt180) cc_final: 0.5042 (ptt90) REVERT: E 56 GLN cc_start: 0.8169 (mm110) cc_final: 0.7909 (mm-40) REVERT: F 141 PHE cc_start: 0.7768 (m-10) cc_final: 0.7528 (m-80) REVERT: G 128 ARG cc_start: 0.9438 (ttp-110) cc_final: 0.9234 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1255 time to fit residues: 30.1031 Evaluate side-chains 104 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 168 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** 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 = 0.4016 r_free = 0.4016 target = 0.097197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.076485 restraints weight = 66209.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.077427 restraints weight = 45222.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.078486 restraints weight = 33162.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.078703 restraints weight = 28516.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.078829 restraints weight = 27076.491| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15323 Z= 0.145 Angle : 0.769 9.183 20853 Z= 0.377 Chirality : 0.048 0.198 2471 Planarity : 0.007 0.059 2520 Dihedral : 5.658 18.854 1981 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: -2.09 (0.19), residues: 1827 helix: -0.43 (0.15), residues: 1169 sheet: -4.26 (0.53), residues: 84 loop : -2.78 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 128 TYR 0.032 0.002 TYR G 234 PHE 0.034 0.001 PHE E 334 TRP 0.010 0.001 TRP A 127 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (15309) covalent geometry : angle 0.76855 / 0.38 (20825) SS BOND : bond 0.00368 / 0.22 ( 14) SS BOND : angle 1.20845 / 0.71 ( 28) hydrogen bonds : bond 0.03916 / 2.52 ( 736) hydrogen bonds : angle 4.91050 / 3.32 ( 2187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8810 (mtm) cc_final: 0.8512 (ttm) REVERT: A 56 GLN cc_start: 0.8029 (mm110) cc_final: 0.7167 (mm-40) REVERT: A 128 ARG cc_start: 0.9460 (ttp-110) cc_final: 0.9190 (ttp-110) REVERT: A 272 ILE cc_start: 0.9285 (pt) cc_final: 0.8956 (pt) REVERT: B 56 GLN cc_start: 0.8079 (mm110) cc_final: 0.7297 (mm-40) REVERT: B 128 ARG cc_start: 0.9440 (ttp-110) cc_final: 0.9144 (ttp-110) REVERT: B 272 ILE cc_start: 0.9185 (pt) cc_final: 0.8840 (pt) REVERT: C 56 GLN cc_start: 0.8312 (mm110) cc_final: 0.7847 (mm-40) REVERT: D 56 GLN cc_start: 0.8138 (mm110) cc_final: 0.7863 (mm-40) REVERT: D 141 PHE cc_start: 0.7825 (m-10) cc_final: 0.7454 (m-80) REVERT: D 152 ARG cc_start: 0.5308 (ttt180) cc_final: 0.5019 (ptt90) REVERT: E 56 GLN cc_start: 0.8198 (mm110) cc_final: 0.7755 (mm-40) REVERT: E 128 ARG cc_start: 0.9622 (tmm-80) cc_final: 0.9278 (ttp-110) REVERT: F 56 GLN cc_start: 0.7958 (mm110) cc_final: 0.7493 (mm-40) REVERT: F 128 ARG cc_start: 0.9247 (ttp80) cc_final: 0.9019 (ttp-110) REVERT: F 272 ILE cc_start: 0.9357 (pt) cc_final: 0.9123 (pt) REVERT: G 56 GLN cc_start: 0.8366 (mm110) cc_final: 0.7927 (mm-40) REVERT: G 128 ARG cc_start: 0.9510 (ttp-110) cc_final: 0.9288 (ttp-110) REVERT: G 280 ASN cc_start: 0.8877 (t0) cc_final: 0.8452 (t0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1153 time to fit residues: 27.5875 Evaluate side-chains 113 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 35 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 33 optimal weight: 0.0670 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 108 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 HIS ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 332 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.095962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.078978 restraints weight = 65286.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.078939 restraints weight = 50644.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.079346 restraints weight = 49099.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.079463 restraints weight = 33518.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.079781 restraints weight = 30884.854| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15323 Z= 0.144 Angle : 0.757 9.238 20853 Z= 0.368 Chirality : 0.047 0.189 2471 Planarity : 0.006 0.058 2520 Dihedral : 5.529 18.579 1981 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.19), residues: 1827 helix: -0.21 (0.15), residues: 1169 sheet: -4.36 (0.55), residues: 84 loop : -2.74 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 217 TYR 0.026 0.002 TYR G 234 PHE 0.031 0.001 PHE F 141 TRP 0.012 0.001 TRP D 127 HIS 0.001 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (15309) covalent geometry : angle 0.75683 / 0.37 (20825) SS BOND : bond 0.00369 / 0.22 ( 14) SS BOND : angle 1.00951 / 0.60 ( 28) hydrogen bonds : bond 0.03734 / 2.43 ( 736) hydrogen bonds : angle 4.82098 / 3.26 ( 2187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8614 (mtm) cc_final: 0.8179 (ttp) REVERT: A 56 GLN cc_start: 0.7883 (mm110) cc_final: 0.7006 (mm-40) REVERT: A 128 ARG cc_start: 0.9284 (ttp-110) cc_final: 0.8994 (ttp-110) REVERT: A 217 ARG cc_start: 0.8895 (mtm180) cc_final: 0.8636 (mtm110) REVERT: A 272 ILE cc_start: 0.9245 (pt) cc_final: 0.8831 (pt) REVERT: B 56 GLN cc_start: 0.8017 (mm110) cc_final: 0.7213 (mm-40) REVERT: B 128 ARG cc_start: 0.9366 (ttp-110) cc_final: 0.9059 (ttp-110) REVERT: B 272 ILE cc_start: 0.9140 (pt) cc_final: 0.8733 (pt) REVERT: C 56 GLN cc_start: 0.8002 (mm110) cc_final: 0.7504 (mm-40) REVERT: D 56 GLN cc_start: 0.7996 (mm110) cc_final: 0.7736 (mm-40) REVERT: D 141 PHE cc_start: 0.7588 (m-10) cc_final: 0.7221 (m-80) REVERT: D 152 ARG cc_start: 0.5543 (ttt180) cc_final: 0.5209 (ptt90) REVERT: E 40 CYS cc_start: 0.8913 (t) cc_final: 0.8654 (t) REVERT: E 56 GLN cc_start: 0.7854 (mm110) cc_final: 0.7550 (mm-40) REVERT: F 56 GLN cc_start: 0.7740 (mm110) cc_final: 0.7306 (mm-40) REVERT: F 128 ARG cc_start: 0.9148 (ttp80) cc_final: 0.8939 (ttp-110) REVERT: F 272 ILE cc_start: 0.9359 (pt) cc_final: 0.9041 (pt) REVERT: G 56 GLN cc_start: 0.8083 (mm110) cc_final: 0.7625 (mm-40) REVERT: G 280 ASN cc_start: 0.8709 (t0) cc_final: 0.8224 (t0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1158 time to fit residues: 28.2650 Evaluate side-chains 106 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** 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 = 0.3978 r_free = 0.3978 target = 0.094687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.072785 restraints weight = 65335.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.074417 restraints weight = 42492.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.075562 restraints weight = 31984.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.076143 restraints weight = 26610.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.076640 restraints weight = 23992.020| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15323 Z= 0.178 Angle : 0.795 9.067 20853 Z= 0.389 Chirality : 0.050 0.213 2471 Planarity : 0.006 0.059 2520 Dihedral : 5.662 20.271 1981 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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: -1.72 (0.19), residues: 1827 helix: -0.03 (0.15), residues: 1162 sheet: -4.48 (0.53), residues: 84 loop : -2.83 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 128 TYR 0.021 0.002 TYR G 234 PHE 0.028 0.001 PHE A 334 TRP 0.020 0.001 TRP D 127 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (15309) covalent geometry : angle 0.79490 / 0.39 (20825) SS BOND : bond 0.00499 / 0.30 ( 14) SS BOND : angle 1.06817 / 0.68 ( 28) hydrogen bonds : bond 0.03878 / 2.50 ( 736) hydrogen bonds : angle 4.87533 / 3.29 ( 2187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8697 (mtm) cc_final: 0.8422 (ttm) REVERT: A 128 ARG cc_start: 0.9420 (ttp-110) cc_final: 0.9148 (ttp-110) REVERT: B 56 GLN cc_start: 0.8146 (mm110) cc_final: 0.7332 (mm-40) REVERT: B 128 ARG cc_start: 0.9439 (ttp-110) cc_final: 0.9121 (ttp-110) REVERT: B 272 ILE cc_start: 0.9289 (pt) cc_final: 0.8851 (pt) REVERT: C 56 GLN cc_start: 0.8207 (mm110) cc_final: 0.7753 (mm-40) REVERT: D 56 GLN cc_start: 0.8171 (mm110) cc_final: 0.7876 (mm-40) REVERT: D 128 ARG cc_start: 0.9321 (ttp-110) cc_final: 0.9072 (ttp-110) REVERT: D 141 PHE cc_start: 0.7805 (m-10) cc_final: 0.7520 (m-80) REVERT: E 128 ARG cc_start: 0.9444 (ttp-110) cc_final: 0.9168 (ttp-110) REVERT: F 56 GLN cc_start: 0.8100 (mm110) cc_final: 0.7479 (mm-40) REVERT: F 128 ARG cc_start: 0.9204 (ttp80) cc_final: 0.8922 (ttp-110) REVERT: F 272 ILE cc_start: 0.9448 (pt) cc_final: 0.9066 (pt) REVERT: G 56 GLN cc_start: 0.8181 (mm110) cc_final: 0.7770 (mm-40) REVERT: G 128 ARG cc_start: 0.9437 (ttp-110) cc_final: 0.9210 (ttp-110) REVERT: G 280 ASN cc_start: 0.8848 (t0) cc_final: 0.8349 (t0) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1069 time to fit residues: 25.5695 Evaluate side-chains 100 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN B 106 HIS ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN F 106 HIS F 280 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.096192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.076659 restraints weight = 66011.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.076904 restraints weight = 45552.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.077220 restraints weight = 35791.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.077852 restraints weight = 33999.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.077839 restraints weight = 29722.264| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15323 Z= 0.141 Angle : 0.781 9.574 20853 Z= 0.374 Chirality : 0.049 0.205 2471 Planarity : 0.006 0.057 2520 Dihedral : 5.536 19.946 1981 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -1.56 (0.20), residues: 1827 helix: 0.11 (0.15), residues: 1162 sheet: -4.45 (0.53), residues: 84 loop : -2.78 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 217 TYR 0.021 0.002 TYR G 234 PHE 0.018 0.001 PHE A 334 TRP 0.014 0.001 TRP D 127 HIS 0.002 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (15309) covalent geometry : angle 0.78107 / 0.37 (20825) SS BOND : bond 0.00322 / 0.19 ( 14) SS BOND : angle 0.82409 / 0.48 ( 28) hydrogen bonds : bond 0.03733 / 2.42 ( 736) hydrogen bonds : angle 4.76520 / 3.22 ( 2187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8788 (mtm) cc_final: 0.8500 (ttm) REVERT: A 56 GLN cc_start: 0.8175 (mm110) cc_final: 0.7244 (mm-40) REVERT: A 128 ARG cc_start: 0.9445 (ttp-110) cc_final: 0.9147 (ttp-110) REVERT: A 217 ARG cc_start: 0.9057 (mtm180) cc_final: 0.8527 (mtm-85) REVERT: A 272 ILE cc_start: 0.9285 (pt) cc_final: 0.9005 (pt) REVERT: B 56 GLN cc_start: 0.8239 (mm110) cc_final: 0.7478 (mm-40) REVERT: B 128 ARG cc_start: 0.9488 (ttp-110) cc_final: 0.9169 (ttp-110) REVERT: B 213 TYR cc_start: 0.8777 (t80) cc_final: 0.8554 (t80) REVERT: B 272 ILE cc_start: 0.9252 (pt) cc_final: 0.8827 (pt) REVERT: C 37 MET cc_start: 0.7782 (mtp) cc_final: 0.7457 (mtp) REVERT: C 56 GLN cc_start: 0.8265 (mm110) cc_final: 0.7859 (mm-40) REVERT: D 56 GLN cc_start: 0.8223 (mm110) cc_final: 0.7950 (mm-40) REVERT: D 128 ARG cc_start: 0.9314 (ttp-110) cc_final: 0.9079 (ttp-110) REVERT: D 141 PHE cc_start: 0.7686 (m-10) cc_final: 0.7440 (m-80) REVERT: E 128 ARG cc_start: 0.9473 (ttp-110) cc_final: 0.9208 (ttp-110) REVERT: F 56 GLN cc_start: 0.8093 (mm110) cc_final: 0.7445 (mm-40) REVERT: F 128 ARG cc_start: 0.9186 (ttp80) cc_final: 0.8896 (ttp-110) REVERT: F 272 ILE cc_start: 0.9400 (pt) cc_final: 0.8997 (pt) REVERT: G 56 GLN cc_start: 0.8269 (mm110) cc_final: 0.7925 (mm-40) REVERT: G 128 ARG cc_start: 0.9483 (ttp-110) cc_final: 0.9265 (ttp-110) REVERT: G 280 ASN cc_start: 0.8799 (t0) cc_final: 0.8309 (t0) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1176 time to fit residues: 30.8300 Evaluate side-chains 113 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 110 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 158 optimal weight: 0.0070 chunk 8 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN B 280 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN F 280 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.095404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.073915 restraints weight = 65715.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.075653 restraints weight = 43036.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.076706 restraints weight = 32088.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.077413 restraints weight = 26921.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.077734 restraints weight = 23992.789| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15323 Z= 0.160 Angle : 0.797 9.463 20853 Z= 0.383 Chirality : 0.050 0.191 2471 Planarity : 0.006 0.058 2520 Dihedral : 5.553 20.098 1981 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1827 helix: 0.15 (0.15), residues: 1169 sheet: -4.55 (0.54), residues: 84 loop : -2.65 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 217 TYR 0.024 0.002 TYR A 284 PHE 0.034 0.001 PHE E 334 TRP 0.015 0.001 TRP D 127 HIS 0.002 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (15309) covalent geometry : angle 0.79632 / 0.38 (20825) SS BOND : bond 0.00431 / 0.26 ( 14) SS BOND : angle 0.92851 / 0.59 ( 28) hydrogen bonds : bond 0.03814 / 2.46 ( 736) hydrogen bonds : angle 4.78644 / 3.22 ( 2187) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.625 Fit side-chains REVERT: A 37 MET cc_start: 0.8691 (mtm) cc_final: 0.8389 (ttm) REVERT: A 56 GLN cc_start: 0.8147 (mm110) cc_final: 0.7831 (mm-40) REVERT: A 217 ARG cc_start: 0.9049 (mtm180) cc_final: 0.8547 (mpp-170) REVERT: B 56 GLN cc_start: 0.8106 (mm110) cc_final: 0.7347 (mm-40) REVERT: B 128 ARG cc_start: 0.9456 (ttp-110) cc_final: 0.9132 (ttp-110) REVERT: B 272 ILE cc_start: 0.9256 (pt) cc_final: 0.8834 (pt) REVERT: C 37 MET cc_start: 0.7748 (mtp) cc_final: 0.7410 (mtp) REVERT: C 56 GLN cc_start: 0.8165 (mm110) cc_final: 0.7814 (mm-40) REVERT: D 56 GLN cc_start: 0.8195 (mm110) cc_final: 0.7947 (mm-40) REVERT: D 128 ARG cc_start: 0.9287 (ttp-110) cc_final: 0.9045 (ttp-110) REVERT: D 141 PHE cc_start: 0.7815 (m-10) cc_final: 0.7569 (m-80) REVERT: E 128 ARG cc_start: 0.9458 (ttp-110) cc_final: 0.9183 (ttp-110) REVERT: E 213 TYR cc_start: 0.8586 (t80) cc_final: 0.8298 (t80) REVERT: F 56 GLN cc_start: 0.7998 (mm110) cc_final: 0.7333 (mm-40) REVERT: F 128 ARG cc_start: 0.9194 (ttp80) cc_final: 0.8885 (ttp-110) REVERT: F 272 ILE cc_start: 0.9359 (pt) cc_final: 0.8936 (pt) REVERT: G 56 GLN cc_start: 0.8163 (mm110) cc_final: 0.7893 (mm-40) REVERT: G 128 ARG cc_start: 0.9450 (ttp-110) cc_final: 0.9219 (ttp-110) REVERT: G 280 ASN cc_start: 0.8844 (t0) cc_final: 0.8333 (t0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1108 time to fit residues: 27.5286 Evaluate side-chains 105 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 101 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.0770 chunk 144 optimal weight: 10.0000 chunk 178 optimal weight: 30.0000 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 280 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN F 280 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.094836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.073272 restraints weight = 65318.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.075035 restraints weight = 42916.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.076101 restraints weight = 31950.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.076775 restraints weight = 26666.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.077202 restraints weight = 23768.948| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15323 Z= 0.171 Angle : 0.805 9.444 20853 Z= 0.389 Chirality : 0.050 0.243 2471 Planarity : 0.006 0.058 2520 Dihedral : 5.616 20.235 1981 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.20), residues: 1827 helix: 0.30 (0.15), residues: 1120 sheet: -4.61 (0.53), residues: 84 loop : -2.52 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 254 TYR 0.023 0.002 TYR E 284 PHE 0.035 0.001 PHE E 334 TRP 0.016 0.001 TRP B 127 HIS 0.002 0.000 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (15309) covalent geometry : angle 0.80468 / 0.39 (20825) SS BOND : bond 0.00466 / 0.28 ( 14) SS BOND : angle 0.88499 / 0.57 ( 28) hydrogen bonds : bond 0.03820 / 2.46 ( 736) hydrogen bonds : angle 4.82049 / 3.24 ( 2187) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8691 (mtm) cc_final: 0.8312 (ttm) REVERT: A 56 GLN cc_start: 0.8165 (mm110) cc_final: 0.7850 (mm-40) REVERT: A 217 ARG cc_start: 0.9063 (mtm180) cc_final: 0.8617 (mpp-170) REVERT: B 128 ARG cc_start: 0.9462 (ttp-110) cc_final: 0.9148 (ttp-110) REVERT: C 37 MET cc_start: 0.7746 (mtp) cc_final: 0.7381 (mtp) REVERT: C 56 GLN cc_start: 0.8125 (mm110) cc_final: 0.7795 (mm-40) REVERT: D 56 GLN cc_start: 0.8281 (mm110) cc_final: 0.8039 (mm-40) REVERT: D 128 ARG cc_start: 0.9290 (ttp-110) cc_final: 0.9039 (ttp-110) REVERT: D 141 PHE cc_start: 0.7746 (m-10) cc_final: 0.7479 (m-80) REVERT: E 128 ARG cc_start: 0.9449 (ttp-110) cc_final: 0.9172 (ttp-110) REVERT: E 213 TYR cc_start: 0.8523 (t80) cc_final: 0.8241 (t80) REVERT: F 56 GLN cc_start: 0.8030 (mm110) cc_final: 0.7361 (mm-40) REVERT: F 128 ARG cc_start: 0.9197 (ttp80) cc_final: 0.8890 (ttp-110) REVERT: F 272 ILE cc_start: 0.9359 (pt) cc_final: 0.8928 (pt) REVERT: G 56 GLN cc_start: 0.8141 (mm110) cc_final: 0.7868 (mm-40) REVERT: G 128 ARG cc_start: 0.9436 (ttp-110) cc_final: 0.9208 (ttp-110) REVERT: G 280 ASN cc_start: 0.8825 (t0) cc_final: 0.8295 (t0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1023 time to fit residues: 24.4191 Evaluate side-chains 96 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 55 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN B 280 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN F 280 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.095300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.073920 restraints weight = 65364.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.075578 restraints weight = 43059.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.076727 restraints weight = 32162.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.077421 restraints weight = 26719.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.077749 restraints weight = 23730.025| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15323 Z= 0.160 Angle : 0.803 9.399 20853 Z= 0.387 Chirality : 0.050 0.237 2471 Planarity : 0.006 0.058 2520 Dihedral : 5.584 20.326 1981 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -1.30 (0.20), residues: 1827 helix: 0.34 (0.15), residues: 1120 sheet: -4.63 (0.53), residues: 84 loop : -2.52 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 128 TYR 0.022 0.002 TYR A 234 PHE 0.034 0.001 PHE E 334 TRP 0.014 0.001 TRP B 127 HIS 0.003 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (15309) covalent geometry : angle 0.80268 / 0.39 (20825) SS BOND : bond 0.00403 / 0.25 ( 14) SS BOND : angle 0.80362 / 0.51 ( 28) hydrogen bonds : bond 0.03800 / 2.46 ( 736) hydrogen bonds : angle 4.77560 / 3.21 ( 2187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.22 seconds wall clock time: 40 minutes 33.38 seconds (2433.38 seconds total)